Clint Dempsey handed the Whites the lead after 107 seconds and the hosts had a two-goal advantage when Damien Duff netted in the 13th minute.
Aaron Wilbraham scored a deflected 77th-minute goal to ensure a nervy ending on the banks of the Thames, which frustrated manager Jol.
"I have to say I had mixed feelings after the game," the Dutchman said. "The first half we were well prepared for them and started off well.
"They changed their system all the time and they do that with a purpose. That was not easy to cope with but I thought we used the right tactics in the first half. There was a good balance between offensive and defensive play. As a matter of fact, we played against their reserves on Monday and we beat them 5-1 and they played in a similar way.
"In the second half they changed their formation and forced us to double-up on the flanks, go back and we couldn't get out of it.
"Of course defenders are used to that in the last couple of years and I think they did tremendously well in that aspect."