Arsenal came into the match trailing 3-1 after the first leg, but wasted no time cutting into their aggregate deficit when Aubameyang poked home a seeing-eye cross from Aaron Ramsey at the near post.
"In the domestic league, like here, we have six teams playing to be in the top four. And the last teams, they are all very important, and it's going to be very hard", Emery said. I said to the players today, I am excited about this competition.
"This game was a tricky situation because at 2-0 up, you're through, but they just need one goal".
"We can be proud of our players today because it was a very hard week - (Manchester) United on Sunday and today against Rennes".
"It is not all like we wanted with the control, but I think as a competitive match, we did very well".
Aubameyang celebrated his second goal, the third on the night, by donning a mask of Marvel superhero Black Panther.
In the past the striker has worn Batman and Spiderman masks to toast goals - but he explained why this time was a special moment.
Arsenal got off to a brilliant start thanks to superstar Pierre-Emerick Aubameyang, who scored in the fifth minute to put Arsenal in the driver's seat.
Rennes, needing only an away goal to take the advantage, looked committed to making a fight of it in the second half and twice hit the post in the first 20 minutes after the break.
"I needed the mask to represent me", Aubameyang said to BT Sport after his sixth brace of the season in all competitions.
"It's a Black Panther and in Africa, in Gabon we call the national team the panthers of Gabon".
"Then he made a challenge on (Ramy) Bensebaini which was also borderline, but the decision didn't go our way. There's a long way to go but with performances like that, we can compete".