The French full-back angled a drive into the far corner from Tom Huddestone's free-kick with just three minutes remaining after we fell behind to a controversial penalty with 83 minutes on the clock.
The spot kick was awarded when Michael Dawson threw himself to his right to block Brian McBride's shot with the ball appearing to strike the top of his chest and shoulder.
The fact 'Daws' leaned into the ball probably didn't help his cause and insult was added to injury when he was booked. Fulham's recent arrival Vincenzo Montella stroked home from 12 yards and it looked like another gloomy day on the banks of the Thames until Chimbonda struck four minutes later.
There were four changes to the team that began against Cardiff in midweek with Lee Young-Pyo, Hossam Ghaly, Teemu Tainio and Jermain Defoe restored to the starting fold.
It was all fairly attritional early on - bar a chance for Ghaly following good work from Berbatov and Defoe - with the most noteworthy features of the game being the barracking given to Steed Malbranque and the Frenchman and Michael Brown snapping into tackles against each other.
Berbatov was looking in the mood for a goal on the road and just tried to take on one man too many on 13 minutes when a shot looked on, although the game lacked a bit of quality cutting edge on a pitch that did not really lend itself to a pure passing game. Tom Huddlestone tried his luck with a piledriver from distance that flashed not too far wide as the team began to assert an authority in the game that was proving a frustration for the home support.
There was a change with the clock on 26 minutes with Didier Zokora replacing a limping Tainio, just after Anthony Gardner failed to direct a good headed chance downwards from a Huddlestone centre. Paul Robinson was then called into action from close range - saving well from Heider Helguson after Moritz Voltz cut back from the right.
Malbranque was then double tagged in lunges from two former teammates that bought a booking for Helguson and the home side were edging back into the contest by using more of their physical advantages going forward - trying to create a bit of mayhem in the penalty area with Helguson and Brian McBride.
Just before half-time Malbranque got booked and Robbo showed what he is all about to prevent us being behind at the break. A whipped cross from Franck Queudrue was met on the full by McBride and Robbo reacted brilliantly from close range.
Having got through to the interval unscathed, Fulham were right back on the offensive early in the second half and what was a feisty encounter was showing no signs of letting up and the home side were soon down to ten men when Helguson was dismissed with a second yellow after a chopping challenge on Huddlestone.
It was then a case of whether the advantage could be made to count, like Fulham did following Dawson's seeing of red here last season. To assist in this, Aaron Lennon was summoned to duty on the hour in place of Ghaly. Seven minutes later Robbie Keane joined the fray.
Chris Coleman made his own change with 20 minutes left to the great approval of three sides of Craven Cottage when Montella was added to the mix.
Lennon was not quickly into the game, but nearly split the Fulham defences on the dash when Chimbonda picked him out before Jan Lastuvka comfortably fielded a Malbranque effort.
On 83 minutes fortune, once again, went against us at this ground when a Gardner headed clearance was struck back at goal by McBride and diverted wide of the upright by Dawson. Referee Mr Dean pointed to the spot and Montella delighted his audience by steering home past Robinson.
Thankfully, that wasn't the final word - that was left to Chimbonda, who provided a cool fnish just when it mattered.
Pascal Chimbonda's first goal for us rescued a point at Fulham after a typically tough encounter at Craven Cottage.