The two-time European champions from Portugal will be in the draw on Thursday while Dynamo will be in the Europa League.
"From the first second we wanted to win and showed it. Now we are happy to be in the Champions League," Benfica coach Roger Schmidt said.
"Let's wait for the draw and then we'll see. It's never easy. I'm happy because we deserve it," he added.
Domestic top-flight football, which had been suspended since Russia's invasion in February and during the ongoing war, returned to Ukraine earlier on Tuesday.
The Dynamo players, who begin their league campaign on Sunday, took to the pitch at the Estadio da Luz draped in the Ukrainian flag in a message of support to their compatriots back home.
Dynamo were already trailing 2-0 from the first leg and they were always on the back foot against last season's quarter-finalists.
Former Manchester City defender Nicolas Otamendi's emphatic header put Benfica ahead on the night in the 27th minute in front of a crowd of more than 58,000 from a Neres cross.
Rafa Silva netted next for the Portuguese side and Brazilian forward Neres swept the ball into the net after a flowing move before half-time.
In the second half Enzo Fernandez's close-range effort was saved by Dynamo goalkeeper Georgiy Bushchan as Benfica wrapped up a convincing 5-0 aggregate win.
Elsewhere, Milan Pavkov's 90th minute own goal secured Maccabi Haifa's spot as they beat Red Star Belgrade 5-4 over two legs.
Jan Kliment's 73rd minute effort booked Viktoria Plzen's place in the draw as they beat Azeris Qarabag 2-1 on aggregate.
On Wednesday, former two-time champions PSV Eindhoven host Rangers with the tie at 2-2, Copenhagen head to Trabzonspor with a 2-1 lead and Bodo/Glimt go to Dinamo Zagreb with a 1-0 advantage.