The 21-year-old wasn't due to be involved against Bristol Bears at Franklin's Gardens but came in at late notice after Paul Hill was forced to withdraw due to illness.
Painter came off the bench in the 57th minute, replacing Owen Franks, but he had to be helped off the field three minutes later.
The tighthead prop tore his calf during a scrum and now faces a lengthy spell on the sidelines.
"He tore a calf muscle so that's a long-term injury for him," Boyd said.
"He wasn't supposed to be in the 23 but Paul Hill succumbed to sickness and Painter came in late.
"Unfortunately, he tore a calf in a scrum.
"It was one of those freak sort of things and we're going to miss him."
It is more bad injury news for Saints, whose forward pack has been decimated in recent weeks.
Courtney Lawes and Lewis Ludlam are with England at the Six Nations, while Jamie Gibson and David Ribbans have been on the long-term injury list.
And last Sunday, lock Alex Moon was added to the treatment room after suffering a knee injury in the eighth-minute of the match.
"We're not going to get Moony, Jamie Gibson or Dave Ribbans back until late March or early April," said Boyd.
"The only relief we're going to get is that Api (Ratuniyarawa) will come back from suspension in three weeks' time."
Francois van Wyk was not in the matchday squad last weekend, but he is fit to play if required at Exeter Chiefs on Sunday.
Alex Coles and Lewis Bean are Saints' only current lock options, but the club are close to securing some second row injury cover with Premiership experience.
Fraser Dingwall, George Furbank and Alex Mitchell have all been with Lawes and Ludlam in the England camp this week ahead of Sunday's game against Ireland.
But Dingwall and Mitchell have now been released and can play for Saints at Exeter.
Dan Biggar is recovering from concussion and could be involved for Wales against France, while Rory Hutchinson is on the bench for Scotland against Italy.
Ollie Sleightholme will miss England Under-20s game against Ireland Under-20s at Franklin's Gardens on Friday night due to a hamstring injury.
But JJ Tonks is fit again and could feature for Saints this weekend.
Piers Francis remains sidelined after suffering concussion against London Irish last month.
But young centre Reuben Bird-Tulloch, a summer recruit from Saracens, is now fit again.
"Piers has had a couple of unfortunate dings and he's going through protocol," Boyd said.
"We're pretty well stocked in that space with Matt Proctor, Rory Hutchinson, Fraser Dingwall, Andy Symons and now Reuben Bird-Tulloch is back from his hand injury.
"It's an area we've got good depth in.
"Reuben was out for 12 weeks because of his hand injury but he's back in full training now and he's a good prospect."