Peter Crouch rose at the back post after 71 minutes to head home Charlie Adam's deep cross at the Britannia Stadium and give the hosts a 1-0 win, but Bruce felt the goal should not have stood.
Crouch had been on the pitch for less than two minutes when he grabbed his seventh Premier League goal of the season, but Bruce claimed that the 34-year-old was in an offside position when the ball was delivered.
"He's offside, my defenders were adamant he was," said Bruce. "There's only Crouch who could've scored a goal like that.
"A 50-yard pass into the penalty box - you're asking defenders to stay high. They’ve done enough because he's offside. Unfortunately, the linesman hasn't seen it that way.
"In big games like today, and big decisions like that, you expect him [Swarbrick] to get it right - which is disappointing."
Bruce acknowledged that Hull had not offered enough in the attacking third of play – they failed to register a single shot on target – but he felt that defeat was harsh on his hard-working side.
He added: "I don't think we ever deserved to win the match, but you don't expect to lose a game like that - not at this level.
"I know they [the officials] have got a very difficult job, under difficult circumstances - they get put under pressure from all sorts of people here.
"But you expect on big decisions to get it right, but he hasn't."
Like his Hull counterpart, Stoke boss Mark Hughes was also critical of the officials for missing an "horrendous challenge" by Maynor Figueroa on Stephen Ireland, but he felt they did get the decision for Crouch's goal correct.
