Carlos Bocanegra headed home the winner from a free-kick as a feisty encounter at Craven Cottage ticked into the 90th minute.
Forced into a number of changes before the game with the likes of Edgar Davids, Teemu Tainio, Lee Young-Pyo and Mido out, we lost Andy Reid after just 20 minutes through injury and then had to cope with the sending off of Michael Dawson for a second bookable offence with 20 minutes left.
However - with Tom Huddlestone on for Reid and making a fine debut in midfield - we looked to be heading away with a hard-earned point until injury time.
Martin said: "It was very even in the first half although I think we looked a bit more dangerous and we played well in the second half.
"I can remember one save from Paul Robinson but in the second half with Lennon on the flank we did well and could have scored.
"I felt Tom Huddlestone came in and did well, Stephen Kelly did well at left back and Aaron was a threat again.
"But we defended too deep on the free-kick and should have kept a higher line like we normally do. On the other hand we had to change organisation after Dawson was sent off.
"We dominated them with our passing game and on the night I felt we deserved more than we got. We were worthy of a point at least."
Martin pinpointed the first yellow card shown to Dawson as the key to his sending off Ã¢â‚¬â€œ it looked a very harsh decision as the defender simply attacked the ball in an aerial challenge with Brian McBride.
"They tried to outmuscle us up front but I don't think that is possible with Ledley King and Michael and the first challenge Dawson made got him booked. That was very disappointing.
"The second foul was probably a booking, the first one wasn't. Heidar Helguson came in maybe seven or eight times with dangerous challenges from the side.
"Dawson is a very fair player and will never use his arms or his elbows. The sending off was harsh and the turning point. We miss him for a game now and we had to miss him for the last 20 minutes of this one."
Even Fulham boss Chris Coleman had sympathy, adding: "The second foul was a definite booking but I'm not sure about the first."
Martin Jol couldn't hide his disappointment after our last-minute loss at Fulham in the Premiership on Tuesday night.