Arsenal lost 3-0 to Pep Guardiola's side for the second time in five days, enduring a thumping in the Premier League at the Emirates Stadium after a humbling Wembley loss in Sunday's Carabao Cup final.
Wenger's men have lost seven games in all competitions in 2018, more than any other Premier League club, Aubameyang seeing a penalty saved by Ederson early in the second half to compound the Gunners' misery.
Aubameyang scored on his Arsenal debut but has not found the net since, while Mkhitaryan was anonymous as City ran riot in a glittering first-half display.
"They need time to adapt," Wenger told a post-match news conference,
"Every game you lose now you are under pressure. They are players who just joined us, I am sure they will do well."
Arsenal had made a positive start at a half-empty Emirates Stadium, snowy conditions contributing to a low crowd, before Bernardo Silva curled home a superb strike to give City the lead.
David Silva added a second and the unplayable Leroy Sane rolled in a third as City became the first team to score three away to Arsenal in the first half of a Premier League game.
"I felt it was a game of top intensity," Wenger said. "We produced physically our highest performance of the season by quite far. Physically the two teams gave a lot.
"I knew the first half would be difficult for us. They took advantage of every defensive weakness in the first half.
"We lost against a top quality team, the best in the country. The fact they are high in confidence and we are low played a big part tonight."
Confidence is a clear issue for Arsenal, who have lost four of their last five games in all competitions, suffering successive defeats at home.
"You go up by stairs but come down by the lift," an enigmatic Wenger said of his side's problems. "We go through a difficult patch, that's football.
"I don't compare it to any other situation I face before. I commit completely and stay committed and focus on the next game."