Second-half strikes from defender Sam Gallagher (52nd minute), substitute Nguyen Van Quyet (71st) and midfielder Hector Vaghaun (83rd) saw Hanoi through to the next round of the ACL play-offs.
Pune FC will now play in Group H of the AFC Cup beginning later in February.
Pune FC had the first best chance of the match in the 19th minute after winger Anthony D'Souza managed to get into the clear on the left, he drilled a low shot which the Hanoi keeper Nguyen Van Cong parried away. The rebound, however, fell for Gabriel Fernandes who continued run inside the box. With the ball awkwardly falling for the Goan, he failed to finish from close range.
At the other end, Pune FC custodian Amrinder Singh kept the visitors at bay with two back-to-back saves denying attackers PT Luong and NN Duy.
More From This Section
Both sides failed to break the deadlock going into the breather.
The second-half saw Pune FC once again going close in the early exchanges. Medio Arata Izumi saw his cross in from the right cleared followed by Dhanpal Ganesh's low shot straight into the keeper.
Thereafter, Hanoi took charge of the proceedings and scored the opener seven minutes after restart. Australian defender Gallagher jumped the highest inside the box and headed home Thanh Luong's corner in from the left.