Goals from Alexis Sanchez and Mesut Ozil saw the Gunners win away, claiming a much-needed three points in their flagging bid to finish in the top four.
Chelsea and Tottenham, the Premier League's top two, have enjoyed success with similar tactical changes and Wenger says a tweak was needed to exploit relegation-threatened Middlesbrough's lack of confidence.
"I felt it added a bit more stability on the long balls," he told Sky Sports. "We faced a direct game and we have been punished a bit on that. It gave the opponents more of the ball.
"Against Palace we had 70% possession but lost. Sometimes we want to have the ball but when a team lacks confidence just to change the system can help believe something different."
The win was only Arsenal second in six games and first away from home in seven across all competitions, moving them above Everton into sixth place on goals scored.
Wenger continued: "We responded well. I think it was not perfect but the commitment and focus was there. At 1-1 we found a response and managed to win.
"It was a big test, Middlesbrough gave everything. It's one of their last chances to stay in the league.
"It [the top four] is mathematically still alive. We knew we needed to win. Now we have a little break with the FA Cup and then we come back again to the league."