Mr. Nilekani said he has submitted his resignation to Prime Minister Manmohan Singh.
"Yes, I have resigned today," he told PTI.
After his exit as CEO of Bangalore headquartered Infosys in 2007, Mr. Nilekani had taken charge as head of UIDAI, mandated to give a billion Indians an identity card, a mammoth exercise that he had been successfully overseeing.
Mr. Nilekani formally took a political plunge on Sunday, when he joined Congress, a day after the party named him as its candidate from Bangalore South, where he is taking on five-time BJP MP Ananth Kumar in a tough battle.
Bangalore South has been a hostile terrain for Congress which had been tasting defeat since the late 1970s, barring in 1989 when former Chief Minister late R Gundu Rao had won.
Weeks before his formal entry into Congress, Mr. Nilekani had begun his campaign facing a daunting task to reach out to 20 lakh plus voters.
Recently, Karnataka BJP had petitioned electoral authorities against Mr. Nilekani, taking exception to his name and picture figuring with Aadhar card advertisements, when the Model Code of Conduct is in force.