Television pictures appeared to back the linesman's decision as Pernis touched the ball, but McDonald came in for fierce criticism after the match from both managers.
SFA's head of referee’s development, Hugh Dallas, has defended experienced official McDonald.
Dallas said: "I think the main thing is that the final decision that was taken was correct.
"And the referee is well within his rights to change his mind as long as he has not restarted play.
"Dougie, after having given the decision, then received information from the assistant referee that the goalkeeper had played the ball.
"There is a really good replay of the incident from the offside-line camera, which clearly shows the ball changing direction - and that was something that Dougie did not enjoy at the time.
"So the decision was overturned and it's not the first time that has happened this season. It's already happened down at Kilmarnock, where the assistant referee and fourth official overturned a penalty decision."
United boss Peter Houston accused McDonald of being "very inconsistent" after the game and claimed the referee was quick to give penalties against his team.
But Dallas said: "We criticise match officials when they get things wrong and here we are criticising them when they get things right."
Hooper went on to snatch a late winner but Celtic boss Neil Lennon claimed the situation was "unacceptable" after speaking to McDonald during the game.
However, Dallas claimed that Lennon had changed his opinion after further discussion.
"Neil Lennon took the time to go to the referee's dressing-room about 40 minutes after the match was concluded," the former World Cup referee said.
"They had a discussion and Neil accepted that the decision was correct. It was just unusual.
"I think Neil was extremely frustrated that he did not have the opportunity to get an explanation at that time, which is not possible.
"He received a full explanation, which he found acceptable, after the match."