Fulham are 2-1 up against Sunderland after a frantic first 45 minutes at the Stadium of Light.
Ashkan Dejagah was brought down by Craig Gardner but after initially appearing to wave away Fulham protests, referee Mark Halsey elected to award a spot kick.
Berbatov coolly slotted past Simon Mignolet for his 10th goal of the season.
Fulham claimed a two-goal advantage after 33 minutes when Sascha Riether stormed forward to turn home Dejagah's cross on the counter.
Sunderland were handed a lifeline just two minutes later when Halsey pointed to the spot for a second time.
Phillipe Senderos looked bemused after being penalised for a push in the area, with Garnder making no mistake from the spot to reduce the deficit.
