While Mr Naidu was the proposer, YSR Congress Party's Mekapati Rajamohan Reddy seconded Mr Kovind's fourth set of nomination papers.
Union Minister for Parliamentary Affairs Ananth Kumar and a few other BJP leaders, including party general secretary Bhupinder Yadav, were also present there.
"We are confident that our nominee, who is widely acceptable to one and all as he is the most suitable candidate, will get elected by a comfortable margin," Mr Naidu said after filing the papers before the Lok Sabha secretary general, who is the returning officer for the July 17 presidential election.
He said important political parties like JD(U), BJD, TRS and both the factions of the AIADMK have come forward to support the NDA nominee.
Mr Kovind is currently campaigning in various parts of the country, and meeting MPs and MLAs to garner support.
He had on June 23 filed three sets of nomination papers.
Today is the last date for filing of nominations.