The 26-year-old was brought back into the fold by Arsene Wenger for the game at Vicarage Road after suffering a groin problem in his last outing against Chelsea.
That injury ruled him out for a month and forced him to miss the concluding World Cup qualifiers against Slovenia and Lithuania.
He was to last just an hour upon his return to action before limping from the field with a muscle complaint to be replaced by Mesut Ozil.
Welbeck has struggled with fitness issues throughout his time with the Gunners since joining from Manchester United in 2014.
He was forced to miss the 2015 FA Cup final after picking up an injury, with that problem eventually keeping him out for 10 months.
Another problem then kept him out of Euro 2016 with England, with another eight months spent on the sidelines.
It remains to be seen how serious his latest knock is, but Welbeck will be cursing his luck as he fails to add continuity and consistency to his game.