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The Gunners extended their unbeaten run to 17 matches with victory after they had drawn their last three Premier League fixtures.
Aubameyang slid in to tuck home and seal a 2-1 win after Joshua King had equalised for Bournemouth following a remarkable Jefferson Lerma own goal.
“We thought about how we could be better with a very demanding match with physicality and intensity and we decided [to not play him],” Emery explained afterwards.
“Also, today we played with three centre-backs, like some moments in the season we will work like this and it’s another possibility for improvement, to find our best performance in the squad.”
Arsenal have not tasted defeat since August and are now just a point outside the top four – with Emery happy with the display on the south coast.
“Today is 17 matches we haven’t lost, but the last three matches we drew,” he said.
“We know that is not enough for us, for our objectives. We were speaking during the week and above all in the two days before the match that it was very important today.