Winger Ryan Longman appeared to have taken the ball out of play when he crossed from the left after 17 minutes.
But linesman Akil Howson waved play on and Honeyman could not miss inside the six-yard box.
Birmingham’s cause was not helped on 43 minutes when Gary Gardner was shown a straight red card after a bad foul on Greg Docherty close to the halfway line.
Referee Tony Harrington might also have sent him off for an alleged headbutt on Josh Magennis from the resulting skirmish.
Birmingham manager Lee Bowyer had good reason to argue with the officials at half-time following Hull’s opening goal, but his team were poor from the outset – even with 11 men.
And once they conceded a second after 57 minutes, when Mallik Wilks headed home Keane Lewis-Potter’s excellent cross towards the back post, a home win was inevitable.
The visitors admittedly had their moments during an open first half, but Hull were by far the more dynamic side inside the final third.
Indeed, the hosts’ enterprising approach to the game was rewarded when Honeyman scored a slightly surreal goal.
Longman did exceptionally well to wriggle and writhe through a ruck of players on the left before sending across the face of goal a low cross.
Birmingham’s backline – with arms raised and expecting a goal-kick – failed to react.
This allowed Honeyman the chance to flick home from close range.
Furious Birmingham fans might have expected a reaction, but it did not arrive as Hull went for the jugular.
Indeed, the Tigers should have made more of their position of power when Wilks dithered in a lovely position when he should have at least teed up a team-mate.
Though the hosts dominated for most of the game, Birmingham should still have equalised after 36 minutes.
Scott Hogan – deftly played in on the right by Troy Deeney – was thwarted by the right boot of goalkeeper Nathan Baxter.
That was their best chance all game and once Gardner was sent off, there seemed no way back for the visitors.
And so it proved, as Hull kicked on after the interval with a well-worked goal from Wilks.
With Birmingham perhaps striving for damage limitation following Gardner’s unnecessary sending-off, the game became more compact after Wilks put the game to bed.
Hull have now won back-to-back Championship games, with their supporters enthused by an expected £30million takeover from Turkish media mogul Acun Ilicali before Christmas.
Bowyer will rightly point towards Birmingham’s first goal as being the defining moment, but his side lacked enterprise and deserved to leave East Yorkshire empty-handed.