The Gunners are now just three points behind their London rivals with six games left to play.
Arsenal equalised 11 minutes later through Pierre-Emerick Aubameyang, playing a one-two with Danny Welbeck.
A brilliant display from Danny Welbeck saw Arsenal come from behind to eventually beat relegation-threatened Southampton 3-2 in a gripping encounter at the Emirates Stadium.
Southampton now find themselves in a hard situation, three points from safety in the Premier League. Arsenal will rotate a few players to keep everyone fresh and healthy for the Europa League-or they should, at least-but today's match is still a very good opportunity to collect some points.
Welbeck narrowly failed to get on the end of a Wilshere cross after he hooked the ball back from the byline on 79 minutes.
The game ended on a sour note when both teams had players sent off, as Jack Stephens and Mohamed Elneny were given straight red cards for off-the-ball incidents. In the game we found the resources to win.
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Welbeck missed a great chance to put Arsenal back ahead when he fired over from three yards out after Wilshere had hooked the ball across goal.
It was Charlie Austin who made the breakthrough to draw level, just a minute after being brought on as a sub.
"I've got the utmost respect for Arsene".
"That's down to us", he said.
They now lead their quarter-final tie with CSKA Moscow 4-1 after the first-leg.
"Going into the Europa League on Thursday, it's going to be a hard tie even though we won the home game [4-1]".
But the forward made amends when he headed home the victor from six yards - an opportunity that was harder to convert than the miss he'd endured just minutes earlier. It therefore makes sense for Wenger to treat the Premier League as a second-string competition for the remainder of 2017/18, with sixth place the best Arsenal can realistically hope for.