Vajpayee and senior BJP leader L K Advani proposed Singh's candidacy, praising his leadership skills and wishing him a glorious second innings in the job.
The BJP chief filed his nomination with returning officer O P Kohli at the party headquarters in New Delhi.
Kohli received 15 other nominations all in support of Singh. One of them came from the national executive members of the BJP parliamentary party led by Vajpayee.
"Singh's first innings got over successfully. His second innings will be more glorious. The party's future is bright in his hands. We pledge full support to him," Vajpayee said.
Singh, 55, became head of the saffron party in 2005 from Advani, who was virtually forced by the Sangh to quit in the wake of the Jinnah row.
His interim one-year term passed through a series of crises, ranging from expulsion of several senior leaders to the party losing power in Jharkhand.
But both Vajpayee and Advani, who is understood to have been upset with Singh for allowing the RSS a greater role in the organisation, heaped praise on him for the party's success in civic elections in Uttar Pradesh and assembly and Lok Sabha by-elections in Bihar and Madhya Pradesh.
Advani said he believed the BJP would be successful in the upcoming assembly elections under Singh's leadership.
Singh, Vajpayee and Advani arrived at the party's headquarters to a tumultuous welcome, with drumbeats thudding across and activists setting off fireworks.
In his comments after his re-election to the post, Singh said he would steadfastly stick to his style of functioning.
A staunch proponent of the RSS' core Hindutva ideology, Singh insisted that the BJP is rapidly regaining public trust.
"Common people are increasingly reposing their trust in the party," he said, citing the BJP's spectacular showing in recent civic elections in Uttar Pradesh and in assembly and Lok Sabha by-elections in Madhya Pradesh and Bihar.
The BJP chief, who has ruled out support to any other party to form government in Uttar Pradesh and has instead said the BJP would rather prefer to lead a coalition there, claimed his party would win power in the key state.
He, however, maintained that the party was required to stick to its principles in order to win public support.
"Some may find our style of functioning to be awkward. But there is a set pattern in which the party has to work. I cannot give it up," he said when asked about his views on differences within the organisation.
The BJP chief also announced the party's plans to hold a public rally in Lucknow on December 24, which he said would be addressed by Vajpayee to launch election campaign for Uttar Pradesh assembly elections.
He, however, paused for a while when asked whom the BJP would project its prime ministerial candidate for general elections. "...Lok Sabha elections are far away... both Vajpayee and Advani are there. They are our leaders..." he remarked.
