A Reuters reporter said armored vehicles smashed through one of walls of the compound and that he heard bursts of gunfire and grenades.
Colonel Yuliy Mamchur, the commander of the base, said a Ukrainian serviceman had been injured and that he himself was being taken away by the Russians for talks at an unspecified location.
Asked if he thought he would return safely, he said: "That remains to be seen. For now we are placing all our weapons in the base's storage."
Belbek was one of the last military facilities in Crimea still under Ukrainian control following Russia's armed takeover and subsequent annexation of the peninsula, which has a majority ethnic Russian population and is home to one of Russia's biggest naval bases.
Earlier, the deputy commander of the base, Oleh Podovalov, said the Russian forces surrounding the base had given the Ukrainians an hour to surrender.
After the Russians entered, a Ukrainian officer who identified himself only as Vladislav said:
"We did not provoke this, this was brute force. I do not know whether this base will be formally in Russian hands by the end of the day. "Ever since World War Two, this place has been quiet, and they came in here firing, with APCs and grenades. I am very worried now."
Mamchur, the commander, told his troops he would inform the high command that they had stood their ground.
The soldiers applauded, chanting "Long live Ukraine!"
Many stood to take pictures of each other in front of the Ukrainian flag, which continued to fly over the base.
The Russian takeover of Crimea has been largely bloodless, though one Ukrainian serviceman was killed and two others wounded in a shooting in Simferopol earlier this week.
Ukraine's Defense Ministry said on Friday that Crimea's bases were still formally under Ukrainian control, but most are now occupied by Russian troops and fly Russia's tricolor flag.
Ukraine's east rallies for secession vote
More than 5,000 pro-Russia residents of a major city in Ukraine's east demonstrated on Saturday in favor of holding a referendum on whether to seek to split off and become part of Russia.
The rally in Donetsk came less than a week after the Ukrainian region of Crimea approved secession in a referendum regarded as illegitimate by the Western countries.
After the referendum, Russia moved to formally annex Crimea.
Russia declared Crimea part of its area of military control on Saturday after weeks during which men without insignia, widely recognized to be Russian servicemen, had surrounded strategic locations.
The Defense Ministry in Moscow said the Russian flag was flying over 147 military facilities that were previously Ukrainian.
Russia's Black Sea Fleet has so far taken over 54 of the 67 Ukrainian military vessels in Crimean ports.
The ministry adds that fewer than 2,000 of the more than 18,000 Ukrainian military personnel want to leave Crimea.
With Crimea now effectively under the control of Russian forces, concern is rising that Ukraine's eastern regions will agitate for a similar move.
Russia has brought large military contingents to areas near the border with eastern Ukraine.
Russian President Vladimir Putin has said there is no intention to move into eastern Ukraine, but the prospect of violence between pro- and anti-secession groups in the east could be used as a pretext for sending in troops.
Eastern Ukraine is the heartland of Ukraine's economically vital heavy industry and mining and the support base for Viktor Yanukovych, the Ukrainian president who fled to Russia last month after being ousted in the wake of three months of protests in the capital, Kiev.
Russia and Yanukovych supporters contend Yanukovych's ouster was a coup and allege that the authorities who then came to power are nationalists who would oppress the east's large ethnic Russian population.
"They're trying to tear us away from Russia," said demonstrator Igor Shapoval, a 59-year-old businessman.
"But Donbass is ready to fight against this band which already lost Crimea and is losing in the east."
Donbass is the name for the region of factories and mines that includes Donetsk.
About an hour after the Donetsk rally began, the crowd marched through the city center and assembled before the regional administration building chanting: "Crimea! Donbass! Russia!"
Demonstrators waving Russian flags were faced off by lines of shield-wielding riot police.
Inside, German Foreign Minister Frank-Walter Steinmeier was meeting with local officials.
The demonstrators erected several tents, an ironic echo of the massive tent camp that was established on Kiev's central square after the protests against Yanukovych broke out in late November.
"I'm ready to live in a tent, but I'm not ready to submit to the West, to dance to their tune," said Viktor Rudko, a 43-year-old miner.
The local parliament on Friday formed a working group to develop a referendum analogous to the one in Crimea.
Activists on Saturday passed out mock ballots, although no referendum has been formally called.
A number of leading pro-Russian activists have already been detained by police on suspicion of fomenting secessionist activities.
The country's security services said Saturday that they have arrested Mikhail Chumachenko, leader of the self-styled Donbass People's Militia, on suspicion of seeking to seize authority.
First G7 leader visits Ukraine after loss of Crimea
Another Western ally hosted by Ukraine on Saturday was Canadian Prime Minister Steven Harper.
Harper is the first leader of the G7 group of top industrialized powers to visit Ukraine since Russia moved to annex Crimea, CBC News reported.
Harper made the trip over to Kiev while on a visit to the Netherlands, where he arrived Friday.
He was accompanied in the Ukrainian capital by Foreign Affairs Minister John Baird.
Canada, along with other G7 leaders, has denounced the Kremlin's military moves against Ukraine, as well as the results of last Sunday's Crimea referendum.
The G7 countries will gather next week on the margins of a nuclear security summit at The Hague to consider further responses to the Crimea crisis.
Harper's director of communications, Jason MacDonald, told CBC News Thursday that the prime minister's visit is further "expression of Canada's principled stand on Ukraine."
He also said that Harper's meeting with Ukraine's interim Prime Minister Arseniy Yatseniuk is a chance to show Canada's condemnation of "Russia's illegal occupation of Crimea," and its solidarity with Ukraine ahead of presidential elections on May 25.
On Thursday, Ukraine's ambassador to Canada, Vadym Prystaiko told CBC News that "this visit is a very particular one and the significance of this visit is that Canada has taken the leadership on assistance to Ukraine."
Speaking at a briefing in Kiev after talks with Ukraine's Prime Minister Arseny Yatseniuk, Steinmeier said the international community must not allow the Ukraine-Russia crisis to create a new division of Europe.
He also said that he hoped the first OSCE monitors would arrive in Ukraine to support de-escalation efforts in the next couple of days.
Yatseniuk said Ukraine would need support from Europe, highlighting energy security and possible cooperation with Germany "to help with the modernization and strengthening of Ukraine's armed forces."