Michael Gorman expressed his frustrations on social media after the Colombian had been shown a yellow card by John Beaton for diving in the 1-0 win over Livingston.
The intermediary of Morelos praised the player for his reaction to the decision with footage showing he had been brought down by Livi goalkeeper Max Stryjek.
The striker stepped up late on to net the winner which sent Rangers three points closer to wrapping up the Scottish Premiership title.
"At this point, it’s almost comical," Gorman tweeted.
“SPFL referees clearly treating Morelos unfairly in comparison to other players.
“Incredible restraint shown by Alfredo to not lose his cool after the terrible call.”
It was an incident which angered Rangers boss Steven Gerrard.
He was sent off by Beaton after questioning the referee on the pitch at half-time as he sought an explanation as to why three officials “got it wrong”.
“It’s a blatant penalty, it’s a stonewaller,” Gerrard said. “I’m someone who wants to support officials because we are all human and we will make a mistake.
“But what I can’t stand for at this level is three people making the same mistake. They all had clear views of it. I could see it and I’m the furthest away.
“There are three officials at this level who all got it wrong together – I can’t have that. I asked for an explanation and he (the referee) refused to speak to me. I think I'm entitled to a conversation but obviously not.”