A 79th-minute strike by Wayne Rooney saw Fulham slip to an unlucky defeat at home to league leaders Manchester United on Saturday.

After Philippe Senderos misjudged a long ball forward by Jonny Evans, Rooney took full advantage, curling a shot beyond the reach of Mark Schwarzer and into the far corner.

The result was harsh on Fulham, with Bryan Ruiz hitting the post in the first half, before a brilliant long-range effort by John Arne Riise was tipped over the bar by David De Gea.

Moments before Rooney’s breakthrough, Ruiz saw a header cleared off the line by Rafael. And late on, Senderos’ header from a Damien Duff corner was also nodded off the line by Robin van Persie.

Martin Jol made two changes from Wednesday’s 3-1 win over West Ham United at the Cottage, with Ashkan Dejagah and Chris Baird replacing the injured pair of Dimitar Berbatov and Steve Sidwell. Deadline-day arrival Urby Emanuelson was on the substitutes’ bench.

On a cold night in SW6, Fulham created the first opening of the game on four minutes when Ruiz’s ball over the top sent Hugo Rodallega racing away down the right. The striker pulled the ball back for Dejagah, but the Iran international’s wild swipe of a shot hit a United defender and was cleared to safety.

At the other end, Fulham survived an incredible goalmouth scramble on eight minutes. A corner was met by Jonny Evans, who saw his header saved brilliantly by Schwarzer. The ball fell to Patrice Evra but the Frenchman’s shot cannoned off the bar. Rooney hooked a shot in, which Sascha Riether cleared off the line. Still the danger wasn’t cleared, but Schwarzer eventually did well to hold on to a shot from Evra.

Riise went close to opening his Fulham account on 12 minutes. And what a goal it would have been, the Norwegian’s dipping half-volley from 30 yards being tipped over the bar by De Gea.

In a pulsating opening period, Ruiz was teed up by Riise just outside the box. The Costa Rican’s effort beat De Gea but came off the post.

Brede Hangeland then made a superb last-ditch tackle as Nani shaped to shoot. From the resulting corner, the ball came off the back of Hangeland’s head and landed on top of the crossbar.

On 17 minutes, a Fulham free-kick was only cleared as far as Dejagah who sliced his effort inches wide of De Gea’s left-hand post, before Rooney sent a shot whistling just past the far stick after playing a quick one-two with Van Persie.

It was United’s turn to hit the woodwork on 32 minutes. Nani played the ball to Tom Cleverley on the edge of the box, with the midfielder teeing up Rooney, who saw his shot from 16 yards come back off Schwarzer’s left-hand post.

Three minutes before the break and with United about to take a corner, the Cottage was suddenly plunged into darkness as the floodlights went out. The players trotted off, before the lights came back on five minutes later and the teams returned to play out the remainder of the half.

Fulham were forced into a change at the start of the second half, with Hangeland, who was presumably injured, replaced by Aaron Hughes.

Van Persie sent a header from Nani’s cross straight at Schwarzer in the early stages of the second period, before Giorgos Karagounis should have done better than dragging a shot well wide after Baird had robbed Rio Ferdinand of possession.

Just after the hour mark, Rodallega and Dejagah combined to set up Baird, whose fierce shot from distance was saved low down by De Gea. Baird went into the book on 65 minutes for ending a marauding run by Antonio Valencia after Ruiz had lost the ball in midfield. United then threw a third striker into the mix, with Javier Hernandez coming on for Valencia.

Fulham made their second change of the game on 68 minutes, as Karagounis made way for Emanuelson to make his Whites bow. Three minutes later, Dejagah got down the right and played the ball inside for Riether, with the German’s shot from just outside the box parried away by De Gea. Ruiz was just unable to pounce on the rebound.

Fulham came oh so close to edging in front on 76 minutes. Duff’s corner from the left was flicked on by Baird, with Ruiz’s header being nodded off the line by Rafael.

And it was United who made the breakthrough three minutes later. Senderos didn’t read the bounce of a long ball forward by Evans, allowing Rooney to get in behind. The England man still had a lot to do but, with Hughes backing off, he curled his shot into the far corner.

Fulham made their final change on 81 minutes, with Dejagah replaced by Mladen Petric and in the dying seconds, Senderos saw a header from a Duff corner nodded off the line by Van Persie. United quickly broke, but Schwarzer dived bravely at the feet of Hernandez to deny the Mexican.

The Whites continued to press in the dying seconds, but United held on for the three points.