Callum Wilson thought he'd scored a 94th-minute equaliser against the Gunners on Sunday night before VAR ruled out the goal after the referee judged that David Raya was fouled.
Chris Kavanagh was sent to the pitch side monitor to review the incident by VAR official Darren England and after 17 long replays, totalling four minutes and 17 seconds worth of stoppage the equaliser was wiped off the board.
It is by far the most controversial moment of the Premier League season so far and the decision was ripped apart by several pundits and fans from every club across the table.
However, Rooney defended the call and suggested that the foul was clear as day.
"It's a clear foul," Rooney said on the Wayne Rooney Show.
"You're going to obviously get a lot of people saying they think it should have stood because it's controversial and probably all the (Manchester) City players, staff, fans are going to say it should have stood. And then you're going to get all the Tottenham fans, players, staff saying it shouldn't have stood and of course the Arsenal fans and stuff.
"But it's a clear foul. I think you can clearly see the arm crosses his face and it impacts him getting to the ball. So I think it's the right decision.
"It's the one time I actually think VAR has done a really good job in such an important game. You go anywhere near the goalkeeper and you give a foul.”
Arsenal are now on the brink of the Premier League title whilst West Ham are close to being relegated as they pray that Tottenham do not pick up points against Leeds on Monday night.