Relegation-battling West Ham had a stoppage-time equaliser from Callum Wilson ruled out for a foul by Pablo on Arsenal goalkeeper David Raya.
The check took more than four minutes as video assistant referee (VAR) Darren England watched several replays before sending on-ground referee Chris Kavanagh to the screen.
Speaking on The Rest is Football podcast, Shearer agreed with fellow pundits and ex players Gary Lineker and Micah Richards that the officials ultimately made the right call, but said VAR had failed to bring about an end to inconsistency in officiating.
"I guess some people will think it was a foul, some won't, some will think, 'Where on earth is the consistency?' because we're seeing something like that every single week," Shearer said.
The former England captain added: "We're having this discussion all the time, they're taking far too long. I know it's a hugely important decision, but so is every decision.
Lineker added: "(It was) probably a foul, but that's not quite what they are supposed to be, is it? If I were a West Ham fan, or indeed a Manchester City fan, I think I'd be a little bit angry, because there was a lot of fouling going on at that corner."
Former referee Chris Foy defended the length of time to decision took and praised the officials involved.
"Darren England and Chris Kavanagh worked perfectly together on this. Chris Kavanagh didn't see the action of Pablo on Raya and, quite clearly, he has got his arm across (Raya's) chest. He's got no intention of challenging for the ball, but moreover, he has actually got hold of (Raya's) arm and doesn't let go.
"Chris Kavanagh can't see that – it's a clear non-football action, it has a material impact on the goalkeeper.
"Darren England has looked at that and he took his time and he's been criticised for the amount of time it took. But there was so much to check, because there was a suggestion that Declan Rice had committed a foul - but that was after what had happened to Raya.
"It was really good teamwork – calm, composed.
The decision cost West Ham a goal which could have earned them a priceless point in their fight against relegation, while Arsenal survived to stay five points clear of Manchester City at the top of the table.
Former England and Manchester United striker Wayne Rooney also praised the officials.
Speaking on the Wayne Rooney Show, he said: "It's a clear foul. I think you can clearly see the arm crosses (Raya's) 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."
