Warner gifted Bolton a goal on Wednesday when he dropped the ball at the feet of Heidar Helguson and this time around he gifted Mido a dream debut.
Fulham started brightly in the opening minutes with new signing Hameur Bouazza troubling the Middlesbrough backline with his pace and crosses.
The first chance for the home side came in the second minute when Bouazza crossed from the left which was punched away by Mark Schwarzer as far as Alexei Smertin, but his shot was deflected wide.
The home side continued to mount pressure and made the breakthrough in the 16th minute when Smertin's low cross from the right found Brian McBride, who was unmarked and coolly slotted the ball past a helpless Schwarzer from seven yards.
McBride fell awkwardly after the goal as his standing leg seemed to give way and he was stretchered off with a dislocated knee cap to be replaced by £6million man Diomansy Kamara.
Boro's first chance of the game fell to new signing Mido, but his shot from the edge of the penalty area failed to trouble Warner.
The visitors threatened again minutes later when Andrew Taylor's cross found Lee Cattermole in the area but he failed to keep his head and blasted over from eight yards.
David Healy had a chance to add to his impressive goal tally this season when Smertin's looping ball came in his direction, but Schwarzer was quickly off his line to make a point-blank save.
Deep into stoppage time at the end of the first half, Stewart Downing looked certain to level the scores, but Chris Baird was quickly across to block the ball at the far post.
Middlesbrough were gifted an equaliser ten minutes into the second half when Mido picked up the ball on the edge of the area and his tame shot seemed to be covered by Warner but he failed to collect the ball and it rolled between his legs.
With the points looking like they were going to be shared in a dull and uninspiring second half, Cattermole popped up with a winner two minutes from time.
Jeremie Aliadiere pulled the ball back and found the midfielder unmarked in the box to give Boro their first points of the season.
Late on, Healy though he had levelled the scores but referee Andy D'Urso controversially ruled that the ball did not cross the line.