Stefan Johansen had put the visitors ahead after five minutes with a stunning 18-yard strike before Chris Martin was shown red for an alleged elbow, something that Jokanovic will appeal .
It looked set to be a tough second half but Tom Cairney scored a penalty immediately after the restart before Cameron Jerome got one back, but Floyd Ayite put the finishing touches on the win when he rounded John Ruddy to make it three.
Villa visit on Monday in another big game for Fulham and the boss believes they must refocus their attentions onto the visitors from Villa Park on Monday.
He said: "We played 45 or 50 minutes with one player less than them.
“It’s a complicated place, they have only lost three games all season.
“In this crucial, important moment we are in right now, this situation. We believe in ourselves, we play with confidence and we are fighting for top six.
“We will continue to fight and battle. Now our focus is on Aston Villa.
“All the team arrived in the second half with a defensive mind, we know we have to be organised and support each other, but we expect we are going to find some chances in the offensive transition.
“We caught them a few times, we scored two goals - it’s important for us and it’s a great performance.
“In front of us is another important game. For us we must clear minds, refresh the body and be ready for another challenge in front of us.”