The game had barely started when Seri had a poor pass to Denis Odoi intercepted by Fernandinho who charged towards the Cottagers' goal before laying for Leroy Sane to open the scoring 90 seconds after the kickoff.
Efforts from David Silva and Raheem Sterling wrapped up the victory of an affair that, according to Jokanovic, showed the gulf in quality between both sides.
"We never want to lose the game, but it wasn't an easy day for us,” Jokanovic said after the game.
"How we start the game and second half wasn't easy for us to find something positive.
"The result is completely fair, they show why they are the best team in the world and showed great possession of the ball and great attacking weapons.
"They were fast, strong and played good football.
"We didn't find our best or perfect level and without this level it's not easy to play the football."
Seri will look to atone for his costly mistake in Fulham’s upcoming Premier League fixture against Watford next Saturday.