The Cottagers were forced to come from behind against their rock-bottom opponents after Joe Newell’s early opener was overturned by goals from Stefan Johansen and Floyd Ayite to give them a 2-1 win.
It could have been another goal glut, having fired in nine goals in their previous two games, but Chris Martin saw a penalty saved by Lewis Price and a host of other chances were squandered.
Jokanovic’s men had enough to get the job done, though, and saw his side move to within two points of the play-offs.
He was pleased with that, but was left wanting more.
“At the end of the day I have to happy,” he said. “It was a freaky game for us on a Tuesday night against the bottom of the league, it was hard for us.
“When you get to the end of the game and only have a one-goal lead you get nervous because they can score easily.
“We made enough things and chances – we missed the penalty – to make the game easier for us. We didn’t do it and if you don’t do it you will suffer.
“We played well in the second half, although I was a bit worried when we didn’t get the third goal.
“It is not easy against the bottom team.”
The win moves Fulham closer to the top six and this looks like they year that the Cottagers might finally make a tilt at a return to the Premier League.
But Jokanovic is not getting carried away.
He added: “We take it step by step, I am not getting carried away by where we will finish.”
For Rotherham it was normal service resumed as it was a return to losing ways after a rare win against QPR on Saturday.
They were in the game in the first half, and deservedly took the lead, but ultimate they were not up to the challenge.
“We have worked hard with the lads, we knew they were a very good team,” caretaker Paul Warne said.
“I knew it was a hard ask. We prepared well, the lads believed they were going to get something out of the game, and I thought in the first 20 minutes we were really dangerous on the counter attack.
“We should have gone one up earlier than we did, but I also knew they would keep coming at us. I asked the lads to give me everything and they did.”