Steve Bruce’s side were facing a humiliating early exit in their third qualifying round clash, with the Slovakian side leading on away goals going into the closing stages, having taken an early lead.
But substitute Aluko was on hand to volley home from close range in the 80th minute after Ahmed Elmohamady’s cross from the right had been headed back by Robert Snodgrass.
Elmohamady had brought the Tigers back on terms in the 27th minute as he climbed highest at the far post to head Robbie Brady’s left-wing cross beyond goalkeeper Milos Volesak.
The KC Stadium had been stunned with only two minutes on the clock when a swift counter-attack from the visitors ended with Tomas Malek sweeping Frantisek Kubik’s low cross beyond Allan McGregor.
Last week's trip to Zilina saw the ring-rusty Tigers labour to a goalless draw but they were back on home turf and playing in front of 21,156 excited fans.
Bruce packed his midfield with attacking talent, handing new arrival Snodgrass his full debut and using winger Brady to complement Elmohamady on the other flank.
When some early probing came to nothing, Trencin countered at leisure down the Hull right and Malek was well-placed to receive the low cross and sweep the ball beyond McGregor.
The Slovakians were not sitting back and went close to dealing Hull a double blow when Jakub Holubek stung McGregor's palms.
It was time for Hull to have a go. Set free down the left by Yannick Sagbo, Shane Long pushed the ball inside and powered into the area, but he saw his close-range chip pushed clear.
In the 24th minute they tried again, Jake Livermore releasing Sagbo in behind Trencin right-back Peter Cogley.
But Snodgrass miscued his effort on the cross and, when the ball arrived at Brady's feet six yards out of goal, he twice rattled it against Milos Volesak.
The winger redeemed himself, however, by providing the cross for Hull's equaliser.
Once more exploiting the left side, Brady found the space he needed to pick out Elmohamady, whose powerful header squeezed over the line despite the best efforts of Volesak.
The Tigers had their tails up and the capacity crowd roared as one when Long nodded a Snodgrass corner straight down Volesak's throat with half-time fast approaching.
Five minutes into the second half if it was McGregor who watched the ball spin out for a corner as a clutch of Hull players struggled to close down Haris Hajradinovic.
When the hour mark arrived City fans were getting restless as their heroes toiled in vain around the Trencin box.
There was a cheer when Snodgrass' free-kick from distance got Volesak working again but a bigger one when Tom Ince replaced Alex Bruce to make his home debut.
Hull only had 20 minutes to rescue their European season when the former Blackpool man steamed down the right wing before taking a bad touch and losing control of the ball.
So eager were City fans to see their new man pick up his game and make a decisive impact on the outcome, they barely noticed when Aluko entered the fray for the tiring Long.
They would certainly notice him, in the 80th minute, as Snodgrass headed Elmohamady's cross into the six-yard box for Aluko to prod home on the volley and inspire raptures in the home crowd.