Leandro Trossard scored the only goal at London Stadium, five minutes after Raya denied Matheus Fernandes with a save from a 0.54 xG chance.
Ben White's injury prompted Mikel Arteta to move Declan Rice to right-back before reversing course at half-time, with pundits calling the switch a major mistake.
The result leaves Arsenal on the brink of the Premier League title, though Arteta's in-game decisions face renewed scrutiny before the Champions League final.
Was the 'biggest moment in VAR history' a fair call, or did it unfairly decide a crucial title race match?
Is Mikel Arteta's tactical gambling a fatal flaw that could cost Arsenal their season's biggest prizes?