It was the third meeting between the rivals at the tournament and success for India earned them a ninth title.
Both sides again refused to shake hands - as they had in the two earlier fractious encounters.
The India players did not reappear for the trophy presentation and Indian cricket board (BCCI) secretary Devajit Saikia later said the players refused to accept the winner's trophy from Asian Cricket Council president Mohsin Naqvi, who is also the chairman of the Pakistan Cricket Board.
India captain Suryakumar Yadav said: "It's one thing that I have never seen in my career that a champion team is denied its trophy."
The two nations engaged in a brief military conflict in May, which Indian Prime Minister Narendra Modi referenced when congratulating the players on social media.
Even before that conflict, the cricket teams would only face each other at neutral venues.
Made to bat first, Pakistan started superbly, with Sahibzada Farhan (57) and Fakhar Zaman (46) putting together an impressive opening stand of 84.
They rallied to 113-1 with 44 balls left in the innings, but the collapse that followed would be dramatic and prove pivotal to the outcome.
With the help of left-arm spinner Kuldeep Yadav (4-30) and some poor shots, India took the remaining nine wickets for just 33 runs as a shellshocked Pakistan were bundled out for 146 with five deliveries still left in their innings.
India themselves started badly in their reply and lost three wickets in the opening three overs to give Pakistan hope.
But Tilak Varma calmed things down with a fine unbeaten 69, while Shivam Dube (33) and Sanju Samson (24) provided much-needed support as they triumphed with two balls left.
"It is one of the best innings of my life," said Tilak. "It was a bit pressured, but I wanted to stay in and finish the game."
Pakistan captain Salman Agha said: "It is a tough pill to swallow. We couldn't rotate the strike properly, and that is the reason we didn't get the score we wanted. We need to sort out our batting."
-BBC