The spoils looked set to be shared after former Hull favourite Tom Cairney’s second-half strike had cancelled out Ahmed Elmohamady’s 34th-minute opener.
But City, who dominated the first half, rallied from the setback and deservedly claimed the win after Aluko netted from close range with four minutes remaining.
The Cottagers were thrashed 6-0 on their last visit to the KC Stadium in December 2013, and although they were able to avoid a similar humbling they now have just one point from their opening three games, with Hull on seven.
The hosts brought David Meyler, Aluko and Abel Hernandez back into their first XI and it was the latter who almost made an impact inside the first 30 seconds.
The Uruguayan, who was returning from a three-match suspension for punching Manchester United defender Phil Jones last season, raced onto Tom Huddlestone’s headed through-ball which was only just cut out by Fulham goalkeeper Marcus Bettinelli.
Hull continued to soldier forward although a compact Fulham defence initially meant chances were few and far between, with Kit Symons’ men showing little inclination to attack.
From a corner, unmarked Curtis Davies saw a rasping half-volley skim the top of the crossbar to rouse the crowd, while Hull, through full-backs Moses Odubajo and Andy Robertson, were creating chances from both flanks.
Indeed it was Robertson who provided the assist for the 34th-minute opener, with the left-back collecting the ball from a short corner and providing the cross for Elmohamady to send a towering header at the back post past a despairing Bettinelli.
Another Robertson-Elmohamady combination resulted in the ball being deflected just wide and Hull ended the half in firm command as only a fingertip save from Bettinelli prevented a Hernandez flick from doubling the home side’s lead.
It was the Fulham custodian’s last contribution of the night, though, as a clash with Matt Smith in the build-up saw him stretchered off to be replaced by Andy Lonergan shortly before half-time.
The visitors were a different proposition early in the second half and were only denied a probable leveller when Robertson’s last-ditch interception stopped Ross McCormack getting on the end of Jazz Richards’ cut-back.
From the resulting corner, Shaun Hutchinson sent a header whistling over the bar at the near post before Fulham’s persistence paid off in the 69th minute – although they were grateful for another error from McGregor.
The Scotland goalkeeper, whose gaffe at Wolves on Sunday was widely highlighted, spilled a cross under pressure, and although Hull rode the first wave of attack they failed to clear their lines properly and were out of position when Cairney sent a lovely left-footed strike into the top corner from just outside the area.
McGregor made amends with a diving save from McCormack’s 30-yard free-kick, which proved a crucial stop as Hull, following a surge of pressure in the latter stages, claimed all three points.
Substitute Nikica Jelavic’s header bobbled kindly into the path of Aluko and he calmly slotted home to give Hull their second home win of the season.