Alexis Sanchez pounced to settle the contest in extra time after Nacho Monreal cancelled out Sergio Aguero's second-half opener during the scheduled 90 minutes.
But it was a pair of first-half incidents that festered for Toure, who added to a personal catalogue of impressive Wembley displays.
Aguero had a goal ruled out after Leroy Sane's cross was adjudged to have crossed the byline – replays suggesting it fractionally stayed in – and the Argentina striker also had penalty claims waved away following a challenge from Alex Oxlade-Chamberlain.
"I think the referees have to stop this," said Toure, who had a superb volley tipped against the post by Petr Cech 11 minutes from the end of normal time.
"I am very disappointed. It is not the first time, there have been a couple of times.
"If we have to talk about referees, people are going to say we complain, but when we see the highlights, for me it is very disappointing."
Asked whether Sane's cross stayed in play, Toure responded: "Definitely and it was a penalty and something more. But what can we do?
"If we talk about the referee the FA is going to come in for the punishment if we think like that, but I think I need to sleep and rest and forget this game."
Jose Mourinho's side closed to within a point of their fourth-placed neighbours by beating Burnley 2-0 at Turf Moor on Sunday.
The officials could have a thankless task in a high-pressure atmosphere at the Etihad Stadium and Toure joked that maybe they should stay at home.
"I think Arsenal played well and maybe they deserved the win, but at the end of the day we are very sad because after we see the big mistake of the referee," he added. "All the time – something needs to stop.
"Maybe on Thursday we will have a better referee or play without a referee. I would prefer that."
Toure's long-time midfield colleague David Silva is a major doubt for the derby after sustaining a hamstring injury in a heavy challenge from Arsenal defender Gabriel and City missed the mercurial Spaniard's influence as their Wembley afternoon unravelled.
"What do you do when you have a problem? You have to cope with that," Toure said, having also seen Aguero and Fernandinho limp off moments before Alexis's winner.
"We have a great club, we have a great team and I hope he's going to be fit, but it will be difficult because a hamstring is always tough to recover quickly.
"What we have to do is do it for him. It was sad when he was going off in the first half. He wanted to help us, but we have to keep on going."