Milestone goals from ex-Huddersfield midfielder Adam Clayton and Emilio Nsue - their first strikes for Boro - earned the high-fliers a flattering victory as they moved second in the Championship table, with Town dropping into the relegation zone.
Despite the result, Town were clapped off by the home support at the final whistle, with Wagner - after his first home match in charge - confident that if his side can replicate that performance in future weeks, then positive results will arrive.
On his side's encouraging display, Wagner said: "I accept congratulations for the team. I was very pleased how we played this game, especially the first half.
"The result is ridiculous and a disaster. But the way our team played was another step in the right direction. There was confidence after the first two weeks and the game at Sheffield and the future of this team is good.
"We are doing in the right direction and this was the next step in form.
"I think they took their chances and they only had two in this game. You could see which team was the better team today and the more active with and without the ball and which created more chances. It was my team and that's why I am very proud of the performance.
"The result is ridiculous. But sometimes in football, you don't get what you have to get."
Middlesbrough boss Aitor Karanka admitted that his side's first-half performance was poor on a day when Boro were far from their flowing best as they dug in for the second time in successive games to claim an ugly, yet crucial, win.
Karanka, who dedicated the win to BBC Radio Tees' Boro commentator Ali Brownlee, who is suffering from cancer, said: "I wasn't happy with the first half because we went to the pitch and didn't prepare and went on the pitch and did other things.
"We were not playing the way we like to play and were disorganised. But at half-time, we were winning 1-0, but it could have been 2 or 3-1 to them because they had a lot of chances.
"In the second half, we were more organised and one goal was enough.
"We had problems in the first half. But with the quality we have in the squad, one goal can arrive and it did."