The Scottish Championship leaders were infuriated when Andy Halliday was sent off after celebrating the second goal.
Rangers manager Mark Warburton said he was "mystified" by the decision to show a second yellow card for raising his fist in triumph, deemed an offensive gesture by the match officials.
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Halliday is now suspended for Saturday's game against Falkirk.
The player was clearly furious as he made his way up the tunnel.
He had celebrated Barrie McKay's strike in front of the Morton fans, but television footage did not capture any kind of offensive gesture.
McKay's second-half goal added to a Kenny Miller strike that allowed Rangers to restore their five-point lead over Hibernian at the top of the table.
Morton were spirited and industrious opponents, though, often making life difficult for the visitors at Cappielow.
Morton manager Jim Duffy told BBC Scotland: "On Burns Day, we didn't want to be a poor and timorous beastie and we weren't.
"We made them work hard for it and the most important thing we asked the players was to show commitment and attitude and they did that.
"We had a few crosses and balls into the box. I was more disappointed with our final ball.
"I thought that could have been better, but in terms of work ethic and organisation, commitment, I couldn't ask for more.
"Sometimes you have to accept it if the other team has more in the tank."
Duffy was also unable to shed any light on Halliday's dismissal.
"I really don't know," he said when asked what happened. "I was told he made a gesture to the crowd, but I didn't see it.
"I was more disappointed with the fact that we'd just lost a goal."
Rangers left Cappielow with all three points after beating Morton 2-0 but also nursing a sense of grievance.