The visitors took the lead through substitute Erik Lamela’s stunning rabona goal – one of the best strikes in the history of the fixture – but finished with 10 men when the Argentine was sent off for two bookings.
Mourinho hooked Gareth Bale and Tanguy Ndombele in the second half, having lost Heung-min Son to an early injury, and afterwards said some of his key players went missing at Emirates Stadium.
Mourinho told Sky Sports: “I think we played really bad in the first half. The 1-1 was not a fair reflection of the first half. We were poor.
“Defending bad, no intensity, no pressing, even in terms of creating attacking football, some important players hiding. First half, really bad.”
Arsenal’s winner came from the spot after Davinson Sanchez was penalised for a challenge on Lacazette, with the defender catching the Frenchman after he had miscued a chance.
“In the second half we had space to improve, which we did,” Mourinho added.
“And then it is a question, but an impossible question because they do not speak, for Michael [Oliver, the referee] to answer.
“Probably Paul Tierney too, because he was the VAR. According to Kevin Friend [the fourth official], the referee said he had a clear vision and the VAR did not want to go against him.
“In the second half, we recovered control of the game, made changes to try to win, and then the penalty. And then a second yellow card for Lamela. But in the last 20-25 minutes, the team tried to get a different result.”
Asked for more information on the players who had been “hiding”, Mourinho said: “If they did not do better, it is because they could not do better.
“I am not even going in the direction of individuals because the team is a team, I belong to the team. I am guilty of that first half as [much as] the players. The good thing in that we really improved in the second half. Even before the changes.”
In a separate briefing, Mourinho said Bale and Ndombele lacked intensity and did not press well enough, which prompted him to introduce Moussa Sissoko and Dele Alli from the bench.
Son pulled up inside 20 minutes with a suspected hamstring problem but Mourinho said it was not yet clear how long the South Korean could face on the sidelines.