Chelsea ran out 3-0 winners against the Championship side at Stamford Bridge on Sunday, but Mourinho was originally unhappy with an incident prior to his side's second goal.
The Portuguese felt his team should have been awarded a penalty for handball before Loic Remy found the net, and blasted official Friend in a televised post-match interview.
However, having spoken to Friend, Mourinho moved to retract his earlier comments when speaking in a media conference.
"We had a big penalty in our favour and I was speaking with the referee and I want to apologise for my earlier comments to TV because what he did was great refereeing," said Chelsea's manager.
"He was saw that it was a penalty, he was going to give a penalty, but he saw the ball was going to Remy and he waited a couple of seconds.
"He told me that if Remy did not control the ball or if the ball goes over the bar or the ball was lost then he would have given a penalty. So it was good refereeing.
"I was complaining but it was good refereeing by Kevin. So I apologised."
Chelsea, who remain in contention for four trophies this season, host Newcastle United in their next Premier League game on Saturday.
‘Maybe I’ll be signed by Wrexham, who knows? English football would suit me – if an offer came, I wouldn’t think twice, I’d go immediately’ Euro 2024 cult hero reveals his UK dream
‘Managing Leeds? It was an option that appeared, but it wasn’t the right timing. I decided it wasn’t a good idea to leave the club I was at mid-season’: Premier League boss admits to turning down opportunity to replace Jesse Marsch in 2023
