The Bluebirds broke a run of three successive Championship draws and moved to within three points of the play-off places thanks to the Boro striker’s moment of misfortune in the second minute.
The lacklustre defeat ended Middlesbrough’s resurgent four-game unbeaten run and continued Jonathan Woodgate’s difficult start to his managerial career.
Cardiff had only scored two league goals in the month of September but they got a helping hand to get them off the mark after two minutes.
Josh Murphy used his pace to win a corner which 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.
Middlesbrough failed to register a shot on target during the entire 90 minutes and manager 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,” he said.
“We will be back training on Monday. We will be working hard and we move on to the next game.”
Cardiff: Smithies, Peltier, Morrison, Flint, Bennett, Bacuna, Ralls, Whyte, Paterson, Josh Murphy (Hoilett 46), Bogle (Ward 66). Unused substitutes: Etheridge, Vaulks, Nelson, Tomlin, Mendez-Laing.
Middlesbrough: Randolph, Fry, Ayala, Shotton, Dijksteel, McNair, Clayton (Wing 78), Saville (Browne 73), Johnson (Tavernier 81), Assombalonga, Fletcher. Unused substitutes: Howson, Bola, Walker, Pears.
Referee: D Bond (Lancashire).