The striker was ordered off in the final minute of the match with the defeat putting the Lanarkshire club into a play-off to retain their place in the top flight.
McDonald clashed with Saints striker Thomas Reilly with referee Brian Colvin appearing to issue the red card on the say-so of fourth official Andrew Dallas.
A three match suspension would rule McDonald out of next week’s match against Partick Thistle but more importantly from both legs of the play-off final.
“That would be a travesty because it’s a poor decision,” Motherwell boss Ian Baraclough said about a possible three match suspension. “I’ve seen it back time and time again already. Scott has not made contact, there’s no maliciousness to go and make contact and I think when the officials see it they will agree.
“It’s a massive call at a big time in the season and we will appeal. It won’t be a frivolous appeal either. Scotty’s distraught down there. He’s angry and has every right to be.
“He was expecting a challenge from behind and has gone to hold the man off but that has been deemed as throwing an elbow.
“I’m still not sure who made the decision. I was invited in at the end and they said it as a ?collective. I don’t believe the ?referee saw it as such so he’s going on the people around him, which is quite right.
“But I was in the same position as the fourth official and the linesman – and how you could be sure from that angle is ?something that’s getting at me.
“To be missing someone like that would be a blow to us but it wouldn’t be the end of the world. There are players who can go and affect the game.”
Motherwell will play Hibs or Sevco for a place in the top flight.
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