The Cottagers – who are yet to lose a league game since their 1-0 defeat to Birmingham City on February 4, were in fine form as they gained the upper hand against Simon Grayson at Craven Cottage.
Aluko put his team ahead with a 22nd minute strike before Chris Martin doubled the lead. In the 68th minute, Tom Barkhuizen reduced the deficit for the visitors, while the Nigerian provided an assist for Neeskens Kebano for the winning goal.
However, the 28-year-old midfielder was replaced in the 88th minute by Denis Odoi. With this victory, Fulham are seventh on the Championship log with 61 points from 34 games.
They host Leeds United in their next game on Tuesday. A win for them would brighten their chances of a return to the English topflight.