The London club had been losing by a goal at home - after dominating in the away leg - but came back to win on the night to the delight of their fans.
Ivaca Olic had given Dinamo a mere shadow of hope seven minutes after the break, but with the game over as a contest Fulham ensured that they kept up a fine winning record in Europe.
Steed Malbranque levelled for the London club after a brilliant run and through ball from Bjarni Goldbaek with ten minutes remaining of normal time.
And with the referee looking at his watch Luis Boa Morte stole in to add another win to Fulham's European trail.
Click below to read a match summary:
Fulham 2 -1 Dinamo Zagreb (5-1 aggregate)
