Captain Lees had been set to start against QPR but was withdrawn minutes before kick-off with Dominic Iorfa coming into the side.
And Bullen said it was decided that it was not worth risking further damage to Lees’ hamstring which could have seen him absent for longer.
“His hamstring tightened up,” Bullen said.
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“There was no point taking a chance on that.
"We didn't want to lose him but if you put Tom in and it tears then you’re losing him for six weeks.
“For the sake of one game I think it was the right decision.
“The result did no work out the way we wanted.
“Tom will be in on Sunday for treatment and assessment and luckily enough we’ve not got a game for two weeks.”
Bullen did not feel Lees’ late withdrawal could be used as an excuse for the Owls’ poor performance in which they allowed a lead to slip to suffer back-to-back Championship defeats.
He said: “It doesn’t help but it’s not an excuse. There was no excuse for that.”
Wednesday lead against the run of play thanks to a Steven Fletcher penalty but saw the game overturned with a Jordan Hugill brace in the second half.