First-half goals from Gilberto and Goncalo Ramos set up the victory for the Portuguese outfit, who are regulars in the Champions League group stage.
Benfica were knocked out by Liverpool in last season’s quarter-finals, marking their best run since 2016.
Dynamo have their obvious challenges but kept pushing for a goal, with Oleksandr Karavaev forcing a good save from Odysseas Vlachodimos.
Elsewhere, Qarabag kept alive their hopes of qualifying for the group stage for a second time with a 0-0 home draw against Czech champions Viktoria Plzen.
Qarabag became the first-ever Azerbaijani club to reach the group stage in the 2017-18 edition.
Maccabi Haifa claimed a slender advantage after a 3-2 home win over Serbian champions Red Star Belgrade.
Maccabi are trying to become Israel’s first participant in the group stage since Maccabi Tel Aviv in 2015-16.
Red Star have had a good start to the new season, winning all seven games and led 2-1 after goals from Aleksandar Pesic and Guelor Kang.
But Maccabi responded in the second half with Frantzdy Pierrot, who opened the scoring in the 18th minute, equalizing in the 51st minute.
Tjarron Chery struck the winner in the 61st minute, with Dolev Haziza setting up both second-half goals.