The game was over by half-time as Ross McCormack's clinical finish, Moussa Dembele's header and Tom Cairney's deflected effort put Fulham 3-0 up.
Luke Garbutt almost made it 4-0, the same scoreline from Craven Cottage in September, but sliced wide.
Tjaronn Chery grabbed a consolation, side-footing in from a corner late on.
It leaves Jimmy Floyd Hasselbaink with just two wins from 13 games as QPR boss.
Fulham's win at QPR as it happened
The R's came up against a Fulham side who had won just one match in the Championship since the end of October, leaving them four points above the relegation zone.
Jokanovic, a former team-mate of Hasselbaink at Chelsea, replaced Kit Symons at the end of December but had done little to halt the slide - losing three and drawing two of his opening five matches in charge.
However, QPR were completely blown away in the final 10 minutes of the first half at Loftus Road as McCormack latched onto Cariney's through ball and fired in his 16th league goal of the season before an unmarked Dembele had the simplest of finishes.
Midfielder Cairney then took advantage of more lacklustre defending when he tapped from 12 yards in after Dembele's initial shot had rebounded off the post in first-half injury time.
Fulham goalkeeper Andy Lonergan pulled off two fine saves from Nasser El Khayati and Chery before the Dutchman coolly slotted home in stoppage time.
QPR manager Jimmy Floyd Hasselbaink:
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"It was not acceptable. The fans deserve better.
"We had put the standard down in the previous matches and this was well under that standard. We were making steps forward and I didn't see this coming at all.
"It's two steps back. It's now about starting again, getting things right, taking responsibility and starting to look at ourselves again.
"I'm not going to single out individuals. We are a team, and as a team we were well under par."
Fulham head coach Slavisa Jokanovic:
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"After a month of them suffering, I am happy for our supporters.
"It was a great day for us and I believe we deserved that. At the end we didn't take the chance to get a clean sheet, but that's the only thing we could do better.
"We are working very hard to try to be competitive and concentrated, and this match was very positive for us.
"The players have been working very hard in training and this is good for their confidence - they can start to believe they are really good footballers and can play good football."
Fulham defeated west London rivals Queens Park Rangers for the second time this season to give Slavisa Jokanovic his first win as Whites head coach.