The presidential veto was overridden in a vote of 74 to 39 with 10 abstentions.
"The Seimas decision will be assessed by voters," Grybauskaitė said after the vote.
Speaking at the Seimas on Wednesday, Prime Minister Algirdas Butkevičius said that the new Labour Code was necessary for Lithuania to compete in the world.
He said that if the law took effect, it would be monitored and improved through amendments if needed.
Grybauskaitė in early July refused to sign the new Labour Code into law, saying that the legislation, aimed at liberalizing labor relations, failed to ensure the rights of employees and reinforced "employers' domination".
The government and employers say that the new code will help create new jobs and ensure Lithuania's competitiveness.
The International Monetary Fund said on Tuesday that "abandoning the passed labor code following the presidential veto would be a missed opportunity to achieve needed reforms."
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