Putin hailed Tuesday's agreement on four roadmap accords - which will bolster joint action in areas ranging from trade to fighting terror - after hammering out the details in a four-hour summit in Moscow.
But the two sides notably failed to reach a final accord in easing visa rules and returning illegal immigrants, while tension between Moscow and the EU's newcomer states from the ex-Soviet Baltics also bubbled back to the surface.
"The implementation of the roadmaps would allow us to make important progress towards the construction of a united Europe, with no dividing lines," Putin said in the Kremlin.
The four accords cover a raft of policy areas including the economy; freedom, security and justice; and research, education and culture.
But negotiations remained snagged notably on demands by the 25-nation EU for a firm linkage between an accord to ease visa rules and an agreement on the readmission of illegal immigrants.
EU Commission President Jose Manuel Barroso confirmed that while an overall accord had been agreed on, negotiations would continue on the two key issues.
Luxembourg Prime Minister Jean-Claude Juncker, who holds the EU presidency, used a marital metaphor to indicate that while the EU and Russia have not yet consummated their relationship, they are strongly committed to each other.
"Russia and the European Union are not yet on their honeymoon, but it is true love," he said.
The Moscow summit was aimed
at repairing EU-Russia relations
The Moscow summit was aimed at repairing ties battered in recent years - an attempt to agree on the roadmap accords foundered last year when Russia was angered by perceived EU interference in Ukraine.
But the talks were clouded notably by strains between Russia and the EU's three ex-Soviet Baltic newcomer states Estonia, Latvia and Lithuania, which spend six decades under Soviet rule after the second world war.
And the issue resurfaced starkly at the closing press conference, when Putin warned bluntly that he would not stand for "stupid" demands from Latvia or Estonia.
"Russia is ready to sign border agreements with Estonia and Latvia, but only if they are not accompanied by stupid territorial demands," he said.
The Russian leader at one point rounded on an Estonian journalist who asked why Moscow had refused to apologise for the Soviet occupation of the Baltic states.
Putin pointed out that the Soviet parliament in 1989 condemned the annexation of the Baltics.
"The question is closed. We have made [an apology] once and that is enough," he shot back. "What do you want - for us to repeat this every year?"
"Reconciliation should be the watchword for people living on the same continent - we should today look towards
EU foreign policy chief
Another cause of concern for the EU are so-called frozen conflicts in Russia's ex-Soviet backyard near the expanded bloc's borders, including in Georgia and Moldova. There was no indication of concrete progress on the issue.
Putin underlined the strategic significance of the accord in an address at the start of the Kremlin talks.
"The strategic partnership with the EU is an important priority for Russia. I am convinced that adoption of these road maps which is expected today will allow us to build a greater Europe," Putin said.
The EU-Russia summit came a day after more than 50 heads of state and government gathered in Moscow for ceremonies to commemorate the 60th anniversary of the end of the second world war.
EU foreign policy chief Javier Solana said the troubled past could not be ignored, but must not be allowed to dominate policy now.
"Reconciliation should be the watchword for people living on the same continent - we should today look towards the future," Solana told Moscow's Echo radio.