Arsenal’s first defeat in 12 league games leaves them in second place, two points behind City, while third placed Liverpool are behind Arsenal on goal difference.
With just six games left, champions City are closing in on an unprecedented fourth successive Premier League crown.
City’s rout of Luton on Saturday had knocked Arsenal out of first place.
But the Gunners should have been on a high after Liverpool suffered a shock 1-0 defeat against Crystal Palace just half an hour before kick-off in north London.
Instead, Arsenal produced a spluttering display that could prove fatal to their challenge for a first English title in 20 years.
It has been a dispiriting week for the Gunners, who were held to a 2-2 draw by Bayern Munich in the Champions League quarter-finals on Tuesday, setting up a tricky trip to Germany for the second leg on Wednesday.
After blowing an eight-point lead in the title race last season, Arsenal are in danger of squandering the advantage yet again.
Villa had moved up to fourth place without kicking a ball after Tottenham’s thrashing at Newcastle on Saturday dropped them below Emery’s men on goal difference.
And Villa’s second win in six league games moved them three points clear of Tottenham, who have a game in hand in the race to qualify for the Champions League via a top four finish.
Arsenal had started brightly and Kai Havertz’s low drive was palmed away by Emiliano Martinez before Gabriel Jesus headed into the side-netting from Bukayo Saka’s cross.
Accelerating onto Martin Odegaard’s pin-point pass, Saka took aim from inside the area, but couldn’t test Martinez from an acute angle.
Jubilant Villa
Watkins should have put obdurate Villa ahead when he was allowed to break into the Arsenal area unimpeded for a low strike that cannoned back off the post and ricocheted along the goalline to safety.
Just seconds later, Arsenal were repelled by Martinez’s superb reflex save after Leandro Trossard met Jesus’s cross with a close-range shot that appeared destined for the net until the Argentine keeper stuck out a foot to block it.
As Arsenal’s pressure mounted, Saka curled narrowly past the far post from 12 yards.
But superbly-organised Villa remained resolute, reaching half-time on level terms before Youri Tielemans was inches away from giving them the lead on the hour.
Robbing the careless Zinchenko 20 yards from goal, Tielemans unleashed a blistering shot that hit the bar, then bounced onto the post before cannoning to safety.
Martinez pushed away Jesus’s shot from the edge of the area, but Arsenal were labouring to unlock a Villa defence expertly marshalled by Diego Carlos.
The Emirates crowd grew increasingly frustrated as Villa pushed Arsenal back in the closing stages.
And their fears were confirmed in the 84th minute when Emery’s men snatched the lead.
Lucas Digne’s low cross eluded Arsenal defenders William Saliba and Gabriel Magalhaes, leaving Bailey with the simple task of slotting into the empty net from close-range.
Two minutes and 26 seconds later, Watkins delivered the knockout blow, stealing the ball from Emile Smith-Rowe and clipping a delicate finish past David Raya for his 10th goal in his last 11 league games.
Emery celebrated with a jubilant jig on the touchline, while Arteta stood ashen-faced as Arsenal faced up to a catastrophic loss.
© Agence France-Presse
Photo: Twitter @JacobsBen