Leaders at the two-day EU summit also agreed a climate change deal and an EU-wide economic stimulus plan.
Cowen said: "On the basis of today's agreement ... I am prepared to go back to the Irish people next year. I am confident we will be successful in a second vote".
He said the concessions given by his EU peers - including the retention of a permanent commissioner for Ireland - combined with Europe's response to the financial crisis, should sway Irish opinion towards a "yes" vote next time around.
"We are running the referendum in very challenging economic environment, but any objective analysis would suggest that we are far better able to deal with the current economic and social issues by being a member of the EU," Cowen said.
Ireland is constitutionally bound to ratify the text of the treaty via a referendum.
A second defeat could deal it a fatal blow as all 27 nations must endorse the treaty for it to become law.
Cowen did not set a date for the second plebiscite and said that "further work was still needed" to thrash out the legal basis for the changes before he could commit to naming a date for the second vote.
Nicolas Sarkozy, France's president, and chair of the summit, said: "The Lisbon process is relaunched and the Irish people will be consulted again."
|Cowen believes that the new concessions will sway Ireland towards a 'yes' vote [EPA]
Belgium, Luxembourg, the Netherlands and Spain voiced opposition to the changes at the commission but none blocked the agreement.
In Dublin, Sinn Fein, the Irish republican party, criticised the referendum plans.
Padraig Mac Lochlainn, Sinn Fein's "no" vote campaign director, said the deal was a "sham that not only fails to address the reasons why the people rejected the treaty but it's a package of proposals that deliberately seeks to sell the Irish people a pup".
All but one of the other 26 EU member nations have ratified the treaty through their parliaments, with only the Czech assembly still considering the treaty.