Hull remain 20th in the table, but have not won since their opening game of the season and are now on a 540-minute goalless streak dating back to the victory over Preston North End.
Story of the match
Hull were nearly ahead after just two minutes as Lewie Coyle played an excellent crossfield pass, executed first time on the half-volley, to pick out Keane Lewis-Potter before he blazed the ball high over the bar.
Leighton Clarkson volleyed well wide from a partially-cleared corner for Blackburn, with Tyrhys Dolan showing quick feet before curling a lovely right-footed effort inches wide.
The Tigers were on the front foot the rest of the half as Matt Smith span on a sixpence before seeing a drive blocked by Ayala and Lewis-Potter jinked cleverly away from Dolan before skying over the bar from 25 yards.
The visitors continued to ask questions, Josh Magennis fizzing his shot from the edge of the box that was beaten away by Rovers goalkeeper Thomas Kaminski.
Six minutes before halftime, Dolan made another jinking run and his bending shot was palmed away with one hand by Hull keeper Matt Ingram.
Kaminski held a left-footed attempt by Mallik Wilks and he needed two attempts to gather in Lewis-Potter’s shot from the corner of the box early in the second half.
Hull had a goal disallowed as a stretching Magennis diverted Callum Elder's precise pass past a wrong-footed Kaminski, but he was judged to have been offsides.
Blackburn then had a good spell of play as substitute Reda Khadra shot straight at Ingram and a shot by Dan Butterworth was blocked by Coyle.
Butterworth’s long-range strike was then pushed back out unconvincingly by Ingram and Dolan was unable to do anything with the rebound.
On 61 minutes, the hosts were ahead as Ayala rose highest from a corner by Joe Rothwell to bullet a header past Ingram. Brereton's near-post strike was palmed away by Ingram and Lewis Travis' half-volley was just narrowly wide.
Four minutes after Ayala's goal, Rovers added a second as Brereton picked out the bottom corner with an unerring bending drive from 16 yards out that eluded Ingram.
The hosts went looking for a third, Butterworth shooting into the side-netting and Brereton firing wide while at the other end, Kaminski parried away George Moncur's shot before the midfielder curled another attempt over.
Moncur was looking the most likely man to drag Hull back into the contest and he steered his next attempt wide from outside the box via a deflection and curled another long-range shot wide.
That was the last meaningful action of the game as Blackburn climbed into the top half of the table while the Tigers continue to search for their first goal in six games.
Man of the match: Ben Brereton
He scored Blackburn's second and had other good chances to add to his tally and extend his side's lead.