Meanwhile Watford are on inspired form under boss Marco Silva, with 3 wins and 3 draws from their opening 7 games.
But Cleverley converted after a goalmouth scramble to earn the three points that send Watford up to fourth and drop Arsenal to sixth.
"I have seen the penalty now and I respect the decision of the referee", he said. It came at a moment in the game where it was absolutely important for Watford.
Silva joined Watford before this season from Hull City, where he earned widespread admiration despite being relegated from the Premier League.
"He is not. He is fair, He wins fouls like the best players in the world win fouls".
The opener came soon after as Mertesacker rose to head home Granit Xhaka's corner from six yards out, marking his first league start in nearly 18 months with a rare goal.
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Moments later came the penalty drama, and then in injury time when Andre Carrillo's shot was blocked Cleverley lashed in a dramatic victor.
"We had many situations when we could have scored the second and didn't".
'Not everyone is at the same level physically, but I feel we should have won the game'.
Arsenal were attempting to climb into the top four but instead it is the Hornets who find themselves in the Champions League spots.
"When I looked to change Iwobi with [Jack] Wilshere, Koscielny was not right".
After an unbeaten September, Arsenal have gotten their Premier League campaign back on track after disappointing losses to Stoke and Liverpool.