Cardiff manager Neil Warnock believes his side are finally rediscovering their true form.
Josh Murphy used his pace to win a corner he curled towards the near post. In a desperate bid to clear the danger, Boro striker Fletcher turned towards his own goal and flashed a header past Darren Randolph and into his own net.
Cardiff had two penalty shouts turned down within a minute after Gavin Whyte was shoved by Marvin Johnson and Callum Paterson was barged over in the box but their appeals were waved away by referee Darren Bond.
Omar Bogle hit the bar on his first Cardiff start for 637 days but in the end own goal was enough to take Cardiff's unbeaten run to five matches.
"I've always done well against Boro, going back to my playing days," said Warnock. "You look at their squad and you think goals are going to be hard to get, but I actually think we had all the chances.
"We were a lot more like ourselves today, but we need to continue that, we haven't won away from home but we're getting back to our old selves.
"I have got a great bunch of lads here. When we have got the backing like we have here, there's no better place.
"It would have been nice to have scored more but that's not us. We never make it easy for ourselves. I thought we were dominant and they didn't really get a look-in.
"There were a lot of plusses for us. We played some good football."
Middlesbrough failed to register a shot on target during the entire 90 minutes at the Cardiff City Stadium, and manager Jonathan Woodgate demanded an improvement in front of goal.
"I said before the game you have to match Cardiff physically and I thought we did that throughout the game, but we didn't show enough quality on the ball," he said.
"We didn't create enough chances for our forwards – they were basically starved of the ball.
"We will be back training on Monday. We will be working hard and we move on to the next game."
On Fletcher's moment of misfortune, Woodgate was able to recall experiences of his own.
He added: "I have scored an own goal at the Bernabeu. It happens. We move on and get on with it. Hopefully he (Ashley Fletcher) will score a couple of goals against Sheffield Wednesday.
"The passing wasn't good enough and we show it every day in training and that was the disappointing thing.
"I changed the system and I thought it was the right system to play here even though we lost the game, it was the right decision to make."