Watkins 75 seconds goal send the Midlands clear of their last season savior, and Vila first double win over arsenal since 1992/1993.
The forward scored after just 74 seconds of the match, finishing Bertrand Traore’s cutback with a deflected strike for his 10th league goal of the season.
Arsenal struggled to create clear chances in the first half, but Granit Xhaka’s free-kick forced a full-stretch save from Emiliano Martinez.
Mat Ryan, making his Arsenal debut in goal, kept out two efforts from Watkins shortly after half-time as Villa pushed for a second.
The Australian also made a good save to deny Jack Grealish with 11 minutes remaining.
Arsenal offered more threat in the second half but substitute Martin Odegaard missed their best chance with six minutes remaining when he shot over.
Villa move above Tottenham Hotspur to eighth with 35 points. A second consecutive defeat keeps Arsenal 10th, on 31 points.