The winger started the encounter against his compatriot, Semi Ajayi, who recently penned a permanent deal for the Millers.
However, it was the Nigeria international that would have a final say in the encounter as his left-footed shot from close range found the bottom left corner in the 66th minute to give the Cottagers a victory at the New York Stadium.
Aluko was substituted in the 90th minute with 16-year-old Ryan Sessegnon taking his place.
The 28-year-old has now scored six goals in 38 English second-tier matches for the Craven Cottage outfit, placed seventh in the log with 61 points from 38 games.
In their next league encounter, Fulham will travel to take on Derby County on April 4.