It's now five straight PDL North victories for table-toppers Bluesbcfc.com
On what was a miserable afternoon weather-wise, with the rain lashing down at The Trillion Trophy Training Centre, Blues were forced to come from a goal behind to extend their winning streak to five games in the league.
Hull took the lead just after half-time, before Odin Bailey levelled from the penalty spot. Then Thompson-Sommers struck with time ticking down.
Chances were few and far between in the opening stages, with Hull demonstrating a well-organised defensive unit.
Midway through the half Jack Concannon was brought down on the edge of the area, but Joe Redmond's knuckleball free-kick was deflected wide of the upright.
Blues were generally dominating the play with Ryan Stirk and Caolan Boyd-Munce in particular bossing proceedings.
Hull's first attempt on goal took more than 30 minutes as Tyler Hamilton tried his luck, but it was comfortably saved by Moha Ramos.
A fine intercepting tackle by Geraldo Bajrami on halfway set Blues off on a good attack, but Ryan Burke's curling effort was deflected just wide.
In the 39th minute Burke was the provider, laying the ball off for Stirk whose dipping attempt on the full was well pushed away by Will Mannion, who proved to be a difficult barrier to breach after the break.
As Blues continued to build up a head of steam, the 'keeper was then forced to punch Bailey's dangerous cross away.
Blues made a change at the break, Nico Gordon being withdrawn due to the effects of a nose bleed and dizziness after being struck in the face by the ball. Mitch Roberts came on and Joe Redmond shifted across the right-back.
Hull made a strong start after the interval and were rewarded in the 48th minute, following a corner, when Danny Lupano headed in Matty Jacob's left wing cross.
Blues moved away from their diamond shape to a more regulation 4-4-2, to try and get more width and cause problems down the sides against a resilient Hull.
Blues came through a poor period and went on to dictate. Boyd-Munce had a low, skidding shot from outside the area saved before a superb probing cross into the six-yard box vicinity by Concannon was well dealt with.
It was then another try by Boyd-Munce which led to Blues' equaliser. His shot reared up off a defender and as Miguel Fernandez tried to divert the bouncing, loose ball towards goal, a defender blocked the attempt with his arm.
Subsequently Bailey slotted home the penalty into the bottom right-hand corner, sending the 'keeper the wrong way (72 minutes).
Inspired by their leveller, Blues looked to push on in search of a winner and Concannon was denied by a fine save before Boyd-Munce fired inches wide.
Thompson-Sommers was introduced into the action with 10 minutes left, replacing Bailey, who had trained with the first team on the morning of the game.
He sparked Blues into more threats on goal as Hull were forced to hang in there.
Redmond, high up the pitch, sent in a brilliant ball towards goal for Fernandez, who got a deft touch on it sliding in, but Mannion managed to grab hold at the foot of the far post.
Thompson-Sommers then stood up a good cross from the left for fellow substitute Josh Andrews, who also had a positive impact after entering the fray. Andrews rose high and glanced towards goal but Mannion, flinging himself to the right, palmed the effort away - and excellent save.
There were more half-chances as Blues forced Hull to camp in, and they were finally rewarded in the 90th minute.
Some neat interplay on the edge of the box saw Concannon open up a space for Thompson-Sommers, coming in on the left. He took the short pass in his stride, shaped his body perfectly to sidefoot inside the far post and past Mannion.
Blues: Ramos, Gordon (Roberts ht), Burke, Stirk, Redmond, Bajrami, Concannon, Boyd-Munce, Reid (Andrews 60), Bailey (Thompson-Sommers 80), Fernandez. Subs not used: Bradley-Hurst, Campbell.