Houghton was ruled out for the season after suffering apparent knee ligament damage during last weekend’s 1-1 draw with Luton Town.
The 21-year-old has returned to parent club Chelsea for a full assessment of the injury but is expected to miss much of the rest of 2017.
Ferguson admitted his squad was hurting after the blow but says they can use the disappointing news as added motivation to complete their task of securing promotion this season.
“It’s maybe that we can use it as a group as another motivation to get Jordan a winner’s medal, win the title and certainly we’ll do that,” Ferguson told the Free Press.
“He’s a likeable boy. He’s a very popular lad.
“When something like this happens, clearly he was upset.
“He said his goodbyes on Tuesday and it was quite hard. It wasn’t a very pleasant moment for anyone.”
Ferguson was full of praise for the contribution Houghton has made since arriving at Rovers in early August.
Houghton made 36 appearances for Rovers, scoring one goal.
He made the defensive midfield role his own after being drafted in at late notice to cover for Luke McCullough, who was ruled out for the whole season with a cruciate ligament injury.
Ferguson said: “In terms of how we want to play, Jordan has been so important to it.
“When we lost Luke in the summer, probably to a similar injury, we had to fill that space.
“To be fair, Jordan has been outstanding.
“He’s improved. He wants to learn.
“And he’s a great lad on top of that.
“We’re all gutted for him.”
The severity of Houghton’s injury was no surprise given the manner in which he left the pitch last week.
He was in obvious and considerable pain after falling in a rather innocuous challenge and shook his head after getting back to his feet and attempting to put weight on his knee.
Houghton’s injury is the latest in a catalogue of long term absences this season for Rovers which started last summer.
Gary McSheffrey, Craig Alcock, McCullough, Mathieu Baudry, Marko Marosi and Mitchell Lund have all endured lengthy spells on the sidelines this term.
Despite the plethora of injuries with which he has had to deal, Ferguson says it has never got any easier with each passing victim.
“I’ve got to understand it’s part and parcel of the game but we’ve had so many long term injuries – that’s been the problem,” he said.
“Someone told me it’s a combined games of about 220, if you add up all the injuries and how many games people have missed.
“It’s a lot.”