The 21-year-old has returned to parent club Chelsea for a full diagnosis of the knee injury he suffered during Saturday's clash with Luton Town.
Tests are expected to confirm ligament damage and Rovers have already resigned themselves to being without Houghton for the rest of this campaign.
Houghton said his goodbyes to squad and staff at Cantley Park on Tuesday after making 36 appearances for Rovers this season, netting one goal.
Boss Darren Ferguson admitted it was particularly difficult to bid him farewell in the circumstances and also praised his contribution this term.
"Jordan has gone back to Chelsea and he's definitely out for the season," Ferguson told The Star and Doncaster Free Press.
"Chelsea will have to diagnose the injury but it's terrible news.
"It's terrible news for the lad really.
"My first thoughts were always with him. He was quite shaken up by it to be honest.
"We spoke to him in front of the whole squad and wished him all the best as a group. It was important to do.
"But certainly, it wasn't a nice moment because the lad has done so well for us to suffer the injury like he has.
"We'll have to get on with it but our thoughts are with Jordan because it's a big blow for him."
Arriving on loan just before the start of the season, Houghton was signed to cover Luke McCullough's absence in the defensive midfield role after the Northern Ireland international suffered a cruciate ligament injury in pre-season.
He went on to become one of the most influential members of the squad, and his departure will come as a significant blow to Rovers.
Ferguson added: "We're all so disappointed for him because it came from nothing really as these sort of things do.
"We wish him all the best and hope he recovers as quickly as possible.
"We'll keep in touch with Chelsea and Jordan and find out exactly the outcome of the injury.
"We're not 100 per cent on it just yet but we know he'll definitely miss the rest of the season."
To view Jordan Houghton's career and season stats, click here