The Nigerian got his side’s second goal in the 56th minute to help Slaviša Jokanović’s side move into the play-off zone.
Aluko’s acrobatic volley off Floyd Ayite’s cross gave Fulham the lead after Jack Grealish had levelled Ryan Sessegnon’s opener before Neeskens Kebano sealed the win in the 62nd minute.
With this victory, the Cottagers jump to sixth on the English Championship log with 73 points from 43 games.
They travel to Kirklees Stadium on April 22 for their fixture against third placed Huddersfield Town as they intensify their return to the English Premier League.
For Aluko, he has featured in 42 appearances this season with eight goals to his credit.