The goals helped Arsenal battle back from a 3-1 first-leg deficit.
Ismaila Sarr featured for Rennes's 3-1 win over Arsenal in the Europa League a couple of weeks ago and reports have it that the Gunners made contact with the player immediately after that game. For the Rennes game, Shkodran Mustafi comes into the side in place of the suspended Sokratis, while Petr Cech replaces Bernd Leno in goal, as he has been the regular goalkeeper during cup games for Arsenal this season. He then turned provider as the home side took the lead in the tie, when Ainsley Maitland-Niles headed home on the quarter hour mark.
Unai Emery's men will await their quarterfinal opponent pending the Europa League draw, which will be held at UEFA headquarters in Nyon on Friday.
Aubameyang opened the scoring five minutes in when poking home an Aaron Ramsey cross, coming after some good link-up play between the Welshman and Maitland-Niles down the right.
Click through the mini-gallery above to see pictures of Aubameyang's celebration!
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Rennes defender Damien de Silva admits the players were floored after last night's defeat at Arsenal.
That's because Maitland-Niles' goal should not have stood. "The next match is the most important for us", Emery said.
"For us, today and Sunday, we are aware of playing competitively and I think it is good confidence for us to feel that".
Mkhitaryan slotted the ball down the left to Kolasinac, who in turn set up Aubameyang in front of goal for another simple finish.
It did not matter in the end, though, as Rennes failed to find a way through at the other end.