Eaves came off the bench to direct Eric Lichaj’s cross into the net as the home side celebrated three points.
There was just the one change to the eleven that started against Cardiff City at the weekend, with George Honeyman coming in for Leonardo Da Silva Lopes in midfield. Da Silva was included on the bench, where he was joined by Matthew Pennington who was fit again after missing out against the Bluebirds.
Former Tiger Moses Odubajo started for Wednesday who were without leading scorer Steven Fletcher.
George Long made an early save from Barry Bannan as the visitors looked to set their stall out, before the Tigers’ first chance came from a Kamil Grosicki corner but Jordy de Wijs couldn’t keep his header down at the far post.
Other than that, it was a fairly cagey start from both sides, although another piece of good work from Long denied Sam Winnall and Reece Burke made an important block when Atdhe Nuhiu got a shot away.
At the other end Jarrod Bowen sent a shot just wide before Grosicki won a free kick 30 yards from goal. He took it himself but could only send an effort over the bar.
Grosicki got in behind Odubajo to create the final chance of the opening 45 minutes, but his low cross couldn’t be converted and it remained goalless at the break.
Winnall headed wide from Odubajo’s cross early in the second half, while the visitors also picked up a couple of yellow cards with Kadeem Harris and Nuhiu going into the book.
A first change from the home side saw Eaves replace Josh Magennis and it worked a treat as the Tigers took a 72nd-minute lead. Lichaj delivered the cross, and Eaves delivered the stunning header which found the net via the far post.
The home side’s second change saw Daniel Batty come on for Honeyman.
Wednesday felt they should have had a penalty when Lichaj brought down Jacob Murphy right on the edge of the box, but a free kick was the referee’s decision and Lichaj was the man to head away Bannan’s delivery.
Grosicki had the chance to double the lead when played in by Bowen but a shot was smothered by Keiren Westwood and that was the Polish international’s final involvement before being replaced by Josh Bowler three minutes from time.
Wednesday would have one last big chance to level, and it came in added time. Murphy got the better of Lichaj before pulling the ball back to Adam Reach, but he could only fire over the bar and the three points belonged to the Tigers.
Hull City: George Long; Eric Lichaj ©, Reece Burke, Jordy de Wijs, Brandon Fleming; Kevin Stewart, Jackson Irvine, George Honeyman (Daniel Batty 77); Jarrod Bowen, Kamil Grosicki (Josh Bowler 87), Josh Magennis (Tom Eaves 66).
Subs Not Used: Matt Ingram, Ryan Tafazolli, Matthew Pennington, Leonardo Da Silva Lopes.
Sheffield Wednesday: Keiren Westwood, Liam Palmer, Kadeem Harris (Jacob Murphy 59), Barry Bannan, Sam Winnall (Jordan Rhodes 68), Julian Borner, Atdhe Nuhiu, Adam Reach, Moses Odubajo, Sam Hutchinson (Kieran Lee 77), Dominic Iorfa.
Subs Not Used: Cameron Dawson, Morgan Fox, Joey Pelupessy, Massimo Luongo.
Referee: Mr A. Davies.