Fulham had seen off Dinamo's compatriots Hajduk Split in the first round, but this time were confronted by a side containing Bosko Balaban, on loan from Aston Villa, and one-time Newcastle United midfielder Silvio Maric.
Goce Sedloski, once of Sheffield Wednesday, also started, while the Cottagers brought in Andy Melville at the heart of defence in place of Zat Knight.
Romanian Dimitru Mitu drilled a 25-yard shot well over the Cottagers crossbar after four minutes and nine minutes later Steed Malbranque found Marlet at the far post, but the French striker dragged his shot wide of target.
Ten minutes later wing-back Steve Finnan found himself at the near post, but touched Marlet's cross just over the bar from six yards out.
The Cottagers were boosted 12 minutes before the break as Kristijan Polovanec was red-carded for a cynical tackle on Boa Morte, who threatened to break clear from the halfway line.
However, two minutes later Bosko Balaban had a clear chance to break the deadlock, shooting over from 12 yards after a slip by Andy Melville.
But nine minutes before the interval, Boa Morte made the breakthrough, running on to Malbranque's pass, rounding Tomislav Butina and turning the ball home from a tight angle.
Mitu rattled the woodwork in stoppage time with another fine drive from distance as the Fulham defence backed off.
After the restart Marlet wasted a chance to double the lead, but made up for the miss on the hour as he beat the offside trap to slide the ball into the net past Butina from 15 yards.
The home defence were now open to every Cottagers attack, with the pace of Boa Morte a constant threat before his substitution.
Nineteen minutes from time, Edwin Van der Sar had to tip over a Silvio Maric shot as Dinamo looked for a way back into the tie.
Seven minutes later subs Andrejs Stolcers and Hayles combined to make it 3-0, the Latvian running clear down the left to cross for the striker to fire home from six yards out.
Mitu almost got his reward three minutes from time, but Van der Sar tipped his cute chip away for a corner, as Jean Tigana's men recorded a fine win.
Dinamo Zagreb: Butina, Smoje, Sedloski, Polovanec, Maric, Agic, Olic, Krznar, Mitu, Mikic, Balaban. Subs: Turina, Cesar, Mujcin, Zahora, Petrovic, Kranjcar, Bosnjak.
Fulham: Van der Sar, Ouaddou, Melville, Goma, Brevett, Finnan, Malbranque, Legwinski, Djetou, Marlet, Boa Morte. Subs: Taylor, Inamoto, Clark, Hayles, Knight, Wome, Stolcers.
Referee: Iturralde Gonzalez (Spain) 
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