Second-half substitute Boyd worked his way into the visitors' box as Hull chased an equaliser to David Silva's first-half effort, before going to ground under a challenge from Joe Hart.
Referee Lee Mason waved penalty appeals away, but Hart reacted furiously, confronting the Scotland international as replays showed little - if any - contact had been made.
Manuel Pellegrini's side had seen Vincent Kompany sent off in the early stages but their numerical disadvantage did not haunt them as Edin Dzeko's late effort wrapped up a win.
Afterwards, Bruce leapt to the defence of his player, insisting Boyd was not trying to con the referee and suggesting a foul on the same player soon after could have been penalised.
He said: "There's a difference between simulation and diving, and trying to get out of the road. That's what Boyd is trying to do - nobody's going to stand there with Joe Hart coming at him.
"I think the referee got it spot-on. But the push in the back (by Fernandinho) looked a penalty."
Kompany's early dismissal looked to have given Hull a perfect opportunity to pull off a shock defeat, though Silva scored just four minutes later to settle visiting nerves.
The hosts were ultimately unable to break down Manchester City's stubborn defence, to Bruce's frustration.
He added: "I think the frustration is we have never had a better chance to beat them. In the end it became one of those frustrating afternoons.
"We know how difficult it is to play against 10 men. We needed the game to go 30 or 40 minutes longer before Silva scored - that gave them something to hang onto.
"It's been a difficult week for Manchester City but I have to say they defended fantastically well.
"We just didn't have the quality to break them down but I have to say City defended very, very well and they scored a wonder goal. Silva's was a fantastic piece of individual skill."
