An early penalty from Stewart Downing and a second goal in a week for Tuncay Sanli handed the home side a richly-deserved three points, with Tomas Rosicky netting a stoppage-time consolation for the visitors.
"They were good at taking the space every time they won the ball back," he said. "Players like (Fabio) Rochemback, they know when to foul you.
"They played a cup game today."
On the evidence of the past week, it appears Wenger is beginning to miss talismanic midfielder Cesc Fabregas and other creative players.
Wenger said: "At the moment we miss many in the same area. Maybe it handicaps a bit our creative potential."
Victory eased the pressure on Boro boss Gareth Southgate, who hailed the result as the best of his 18 months in the job.
"It's the best result that we've had because of the manner of the win," he said.
Southgate revealed his masterplan for upsetting the Gunners, saying: "Arsenal have had a period of away games.
"I saw what Newcastle did the other night - I went up there.
"We needed to make sure from the first minute they were going to get exactly the same again and we did that.
"We wanted to be on the front foot against them both in how we attacked and how we defended.
"Because they're a class side and if you allow them time to play, they'll destroy you.
"I felt it was a good afternoon to play them, with people like Fabregas and (Alexander) Hleb missing, and we wanted to make the most of that opportunity."
Downing's penalty handed Boro the lead for only the third time in the Premier League this season and Southgate added: "It's what we've been waiting for.
"It always a chicken-and-egg situation. We're not scoring and it's putting pressure on the defence.
"Both aspects of the team have had to be better and they were today.
"The concentration levels were good. We caused them a lot of problems."