The Cottagers held their own for 55 minutes against a capital rival on Saturday, but the opening goal of the contest swung the tie in Spurs' favour.
A rare mistake from Mark Schwarzer proved to be costly for Fulham, as he allowed a speculative effort from Sandro to slip through his grasp.
Buoyed by that effort, and with the hosts tiring, Tottenham wrapped up a 3-0 win at Craven Cottage courtesy of a quick-fire double from Jermain Defoe.
Jol believes the final scoreline flattered Spurs, with his players having dug deep at the end of a busy week to put in another gutsy display.
He told Sky Sports: "First half we played particularly well, we restricted them and their quality players on the flanks - (Gareth) Bale is a great player but couldn't do what he normally does.
"(Aaron) Lennon and (Clint) Dempsey had very quiet games, which was good. Defoe was waiting for his chances. We had more possibilities than them, so I thought we did okay.
"Then we had the situation with Sascha (Riether) with his injury and we had to change a bit. But I think after the goal it changed a lot."