A spokeswoman for Mr. Barroso said the call was the first time the two men had spoken one-on-one since Mr. Putin came to Brussels in late January.
Since then, EU-Russia ties have soured over the Ukraine crisis and the Kremlin's annexation of Crimea.
The EU said Mr. Barroso urged Russia to take steps to de-escalate the crisis in Ukraine, including disarming pro-Russia separatist groups, halting the flow of people and arms across the border into Ukraine and repealing the law passed by Russia's Duma giving Moscow the right to intervene if Russian minorities in neighboring countries are threatened.
On Thursday, at a news conference in Georgia, Mr. Barroso said Ukraine's new president, Petro Poroshenko, in a phone call voiced concerns to him about an alleged Russian tank incursion into Ukraine.
There has been no independent confirmation of the incident.
A senior EU aide said Friday evening Mr. Barroso raised the issue of the alleged tank incursion with Mr. Putin on Friday but got no substantive reply.
Friday's EU statement didn't mention the bloc's oft-repeated threat that sanctions could be stepped up if Russian pressure on Ukraine increases.
The two leaders, according to the statement, also discussed the stalled gas negotiations between Ukraine and Russia over energy export prices and the debts owed by Kiev to Russian state-owned energy firm OAO Gazprom.
The European Commission president, who was also in Moldova this week, also offered to upgrade trade talks with Russia to ministerial level, according to the EU.
The EU plans to sign broad trade and political agreements with Georgia, Moldova and Ukraine on June 27 but has offered consultations with Russia on the impact of those accords.
"As a way to dispel any concerns, President Barroso offered President Putin the possibility to pursue the continuing bilateral talks with Russia at technical level as well as to hold political level consultations," the EU said in the statement.
Russia has strongly opposed the trade and political deals between the EU and its neighbors.
Technical discussions on the agreement are expected to resume between EU and Russian officials next Monday in Brussels — the first such talks since Russia's annexation of Crimea.
Source: The Wall Street Journal