Arsenal made the ideal start after Maitland-Niles played the ball into Aaron Ramsey who squared for Aubameyang to slot home from close range to put the Gunners 1-0 ahead after only three minutes.
Arsenal became only the second team in Europa League history to win a tie after losing the first leg 3-1.
Aubameyang kept Ramsey's pass in play, but the Gabonese striker looked to be stood in an offside position before picking out Maitland-Niles at the back post.
Petr Cech says winning the Europa League with Arsenal would be the ideal end to his career.
Rennes gave Arsenal a real scare shortly after the half-time restart as Ismaila Sarr picked out the post with his shot, which took a touch on its way through, after Shkodran Mustafi was caught on the ball.
Arsenal responded soon after, though, with Alex Iwobi pulling a shot wide on 70 minutes before Aubameyang finished off a nice move minutes later from a ideal cross from the left by Sead Kolasinac.
And Aubameyang - who has previously celebrated goals with Batman and Spider-Man masks - had a special celebration up his sleeve, wearing Black Panther headgear from the Marvel superhero film.
After 15 minutes of the second leg, it seemed as though Arsenal were going to cruise into the quarter-finals. Well, that was until Aubameyang struck in the second half to complete his brace and extended their lead. He should have had a hat-trick, too, missing two late chances to secure the match ball.
That's when Aubameyang scored his second goal of the game, ensuring that Arsenal would advance on a lovely passing play that beat Rennais' last defender back and the keeper for an easy tap-in to make it 3-0 Arsenal in the match and 4-3 on aggregate. Having been linked with a move to Arsenal at the end of this season, Sarr did not seize his opportunity to shine, with a hopeful shot in the sixth minute of added time his only notable contribution.
Five injured as footover bridge collapses in Mumbai
The bridge, which falls within the Mata Ramabai Ambedkar Marg Police Station, is just two minutes walk from the BMC headquarter. He added that Railways along with the municipal corporation will conduct a joint-investigation regarding the accident.