Alan Pardew's side headed into the game on the back of an impressive 2-1 win at Aston Villa, while Hull were looking for their first away win of the campaign.
The hosts twice grabbed the lead through Loic Remy, making his full home debut at St James' Park, only for Hull to pull things back through Robbie Brady and Ahmed Elmohamady.
And it was the newly-promoted side who would take all three points, Aluko scoring late on to stun the home crowd and send the travelling fans home happy.
Newcastle were unchanged from the side that won at Villa last weekend, but Hull manager Steve Bruce was forced to make two changes to his starting XI.
Defender Liam Rosenior was handed a start in place of Maynor Figueroa, absent on compassionate grounds, while Stephen Quinn replaced the injured Robert Koren.
Newcastle made a quick start to proceedings, with Yohan Cabaye and Mapou Yanga-Mbiwa both shooting over from range in the opening exchanges. And it did not take them long to open the scoring, Remy heading into the bottom corner after Papiss Cisse had directed Moussa Sissoko's far-post cross into his path.
The hosts continued to do most of the pressing, but Hull began to grow more assured as the half progressed, carving out some promising opportunities.
And Pardew's men eventually ceded the initative midway through the first half, Brady firing a low left-footed shot under Tim Krul just moments after the Dutchman had produced a fine save to deny Danny Graham from point-blank range.
Hull dictated matters after finding the equaliser, with the majority of their attacks coming down the left-hand side as they targeted Newcastle right-back Mathieu Debuchy.
However, Bruce's men failed to take advantage of their superiority, and Newcastle re-established their advantage just before the break as Remy fired in his second with a curling strike after Cabaye had seen his initial effort blocked.
Newcastle's lead in fact lasted just two minutes into the second half, as Elmohamady capitalised on some poor defending from the hosts to head Brady's inswinging free-kick in off the post.
The chances dried up following that second leveller, and Newcastle were dealt a blow on the hour mark when Cabaye limped off after coming off worst in a challenge with Curtis Davies.
Hull strangled the life out of the game as the second half wore on, the Yorkshire club controlling the tempo and not allowing Newcastle to create any clear-cut opportunities.
But the visitors did not want to settle for a point, and 13 minutes from time they took the lead in spectacular fashion, Aluko volleying home from close range after great work down the left from substitute George Boyd.
Remy somehow volleyed wide from two yards out in the dying embers but Hull held on to seal a big win.
