Modi, a number of his cabinet colleagues, including Rajnath Singh, M Venkaiah Naidu and Nitin Gadkari besides BJP chief ministers among others proposed Shah's name during the nomination process in which no other leader joined the fray.
Party veterans, including L K Advani and Murli Manohar Joshi, who have in past expressed their unhappiness with 51-year-old Shah's stewardship, were conspicuous by their absence at its headquarters as its almost entire top national and state leaders lined up to greet him.
Modi, who was not present during the exercise due to official engagements, will attend the parliamentary board meeting, likely on January 28, to welcome Shah in his new innings.
Modi congratulated Shah on his re-election and voiced confidence that the party will scale newer heights under his leadership.
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"Congratulations to Shri @AmitShah on being elected BJP president. I am confident the Party will scale newer heights under his leadership," Modi tweeted.
Altogether, 17 nominations were filed proposing the Gujarat leader's name during the three-hour nomination exercise, party vice president Avinash Rai Khanna, who was the chief electoral officer, said as he announced his unopposed election.
All BJP chief ministers, barring the one from Haryana, who was busy in an official engagement, and its state party presidents were present, reflecting the virtually total support Shah commanded.
This will be the first full three-year term for the Gujarat leader, seen to have full backing of Modi, as he had taken over as the party chief in May 2014 after his predecessor Rajnath Singh joined the government.
He also led the party to victory in Jharkhand and Jammu and Kashmir but some of the sheen of his leadership wore off after it suffered crushing defeats in Delhi and Bihar assembly elections, sparking some rumblings within.
However, his aides have argued that he remains the best bet for the party as it faces elections in five states this year and the crucial Uttar Pradesh polls next.