The 23-year-old has scored six times for Salop in League One during his first season at the club, but he was taken off during the win against Morecambe last weekend in the 75th minute after injuring his ankle.
And the Town boss Steve Cotterill has now revealed the attacking midfielder will not feature again this campaign and is set to go under the knife soon.
He said: "Tom will be out for the rest of the season now. He ruptured his ankle ligaments at the weekend, and we're really disappointed about that. Nobody around him, he's just gone down in a hole in the penalty area so we're really, really disappointed with that.
"He's ruptured his ligaments, so he has to have his ankle reconstructed, and that will be him now until pre-season. It's a real blow.
"It will leave us short for today's game and for the rest of the season. I suppose nothing is new there, we've been short for the whole season, but it makes how well the lads have done even more remarkable.
"We must not let this define our season, and Tom will be having an operation to reconstruct his ankle soon. We don't have a date yet because his ankle is still swollen, and it's got to settle down and then we'll have a bit more of an idea."
Bayliss took to Twitter to say he is 'gutted' by the news but he will continue to support the team from afar.
He said: "Absolutely gutted to have my season cut short, loved every minute of getting back to playing week in week out, I’ll be back stronger and ready for the start of next season and I’ll do all I can to support this special team from the sidelines for the rest of this season."