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.
The Gunners need to overturn a 3-1 deficit from the first leg in France, if they seek to progress to the next round.
Nevertheless, Emery said the Champions League, Europe's premier club competition, was not his only focus because the Europa League - which he won three times in a row from 2014 to 2016 as manager of Sevilla - also provides the chance for silverware.
Arsenal will discover their quarter-final opponent at tomorrow's draw in Nyon, with Chelsea, Napoli and Eintracht Frankfurt the teams Emery will be hoping to avoid.
We doubled our advantage just 10 minutes later when Aubameyang combined with Ramsey before crossing for Ainsley Maitland-Niles to head home at the far post for 2-0 in the 15th minute.
The Arsenal striker scored twice as his side eliminated Rennes 3-0 in the Europa League, the continent's second-tier global club competition behind the Champions League.
The ill-tempered feel to the match continued throughout a nervy second half as a number of strong challenges went unpunished. "Sometimes you give a big performance, you do everything right, you are unlucky and you can go out".
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The game kicks off 9 pm West African time.
"We can be proud of our players today because it was a very hard week - (Manchester) United on Sunday and today against Rennes".