Loic Remy had twice given the home side the lead in the first half, finding the net either side of a low Robbie Brady strike.
But Ahmed Elmohamady made the most of some slack marking to level, and Aluko, who was a menace all afternoon, snatched all three points, expertly volleying a George Boyd cross in from the edge of the box.
Remy had a wonderful chance to grab a late point, but spurned his opportunity of a hat-trick from point-blank range to ensure Steve Bruce's return to the north east was a very happy one.
The home side dominated the early stages, with Remy looking particularly threatening on the left of the Magpies' three-pronged attack.
And it was the Frenchman who opened the scoring, heading in from close range after Papiss Cisse had diverted Moussa Sissoko's deep cross into his path.
Everything looked comfortable for Alan Pardew's men after the goal as they played the ball around with ease, with Hull struggling for possession.
Then, out of the blue, moments after Tim Krul had kept out a Danny Graham header from close range, Brady was picked out on the left in space by Sone Aluko, and the Irish midfielder fired the equaliser low past the stranded goalkeeper.
The Tigers were transformed after the goal, offering a real threat, and enjoyed much more of the ball, creating several openings, with Danny Graham guilty of spurning the best chance, with his touch letting him down when played through on goal.
But just before the interval, Remy again gave the home side the lead, side-footing home after Yohan Cabaye's goalbound effort had been diverted into his path.
Just as the Magpies' faithful thought their side were on course to secure their third win in a row for the first time since April 2012, Elmohamady headed Hull level from a Brady free-kick just after the break, with the Newcastle defence conspicuous in their absence.
Once again the visitors seemed buoyed by their goal, and caused Newcastle more problems, with Graham again wasting a great chance to put his side in front, scuffing an effort wide.
And their pressure did eventually tell when substitute Boyd did well to make room for a cross, picked out Aluko 18 yards out, and the lively striker brilliantly beat Krul on the volley to deservedly put the Tigers in front for the first time in the match.
Remy really should have snatched a point late on, but he sliced wide after being picked out in the six-yard area and teeing himself up well.
The Tigers held on to secure all three points and quash Newcastle's hopes of maintaining their fine form, and left Pardew wondering what might have been.