Khudobin skated over to the Bruins bench at Warrior Ice Arena just before practice and had his right arm or wrist attended to by the training staff. The goaltender then left the ice and didn't return.
On Tuesday Bruins GM Don Sweeney announced Khudobin has an upper body injury and is expected to miss approximately three weeks.
The Bruins already were without Tuukka Rask, who has been out since Oct. 20 because of an undisclosed injury suffered in a game against the New Jersey Devils.
Heading into their home game against the Minnesota Wild on Tuesday, the Bruins (3-2-0) didn't know who would be their starting goaltender.
"This is hockey," Bruins coach Claude Julien said. "We deal on a day-to-day basis with injuries. You wait for the news and you go about doing your job as it's required. If we have to make some adjustments and we have to have different personnel, we'll deal with it when we have more of an update. But right now I have nothing."
Julien said Rask is still day-to-day.
Malcolm Subban, the Bruins' first-round pick (24th overall) in 2012, was recalled from Providence of the American Hockey League on Monday to fill in for Rask.
Rask started the Bruins' season opener Oct. 13. He then missed the next game two nights later because of injury, but he was able to dress as Khudobin's backup. Rask returned to play the following two games, but he hasn't skated since he beat the Devils 2-1 on Oct. 20. Rask is 3-0-0 with a .947 save percentage and 1.67 goals-against average.
Khudobin is 0-2-0 with a .849 save percentage and 4.10 GAA.
Subban's emergency call-up couldn't have come at a worse time for the 22-year-old. In four games for Providence, he has a .846 save percentage and 4.50 GAA and he has been pulled twice. He allowed four goals on 34 shots in an overtime loss to Albany on Sunday.
"Obviously not the way you want to start the season," Subban said. "To be honest, last game I felt a lot better. ... I feel like I'm battling. It's not the first time I've faced adversity, it's not going to be the last. I don't feel too down on myself right now, to be honest."
Subban's only previous NHL experience was a start to forget on Feb. 20, 2015, on the road against the St. Louis Blues.
He was pulled one minute into the second period after allowing three goals on six shots.
With the Bruins needing to bounce back from their 4-2 loss to the Montreal Canadiens on Saturday, Subban might get another chance.
"If I get the call, I'll be ready to go," Subban said.
Information from The Associated Press was used in this report.