That victory has seen Fulham rise into the play-offs after Sheffield Wednesday drew 1-1 with Barnsley earlier in the day, but it wasn't easy for Jokanovic's side.
Rotherham frustrated the Cottagers before Aluko managed to get the only goal in the tie in the middle of the second half, but the Millers had the chances to win the game themselves.
But Jokanovic is pleased his side got the result, saying: “It’s a great step for us, after a very tough game.
“We knew we’d have to concentrate to score the goal and finish the game without making too many mistakes.
“I’ve said before that I miss 1-0 victories, and we scored one goal and finished the game with a clean sheet. In the end we found this kind of situation, and this is good news for us.
“We tried to be focused on our job and thinking about what we can do in this competition,” he explained. “We weren’t thinking about Sheffield Wednesday, about teams in front or behind us.
“It’s simple, we tried to focus on our job and try to find our best performance, especially in what is a crucial part of the competition. We must be focused and concentrate on not making mistakes, and try to win as many points as possible.”