The Magpies celebrated club legend Pendlebury becoming the all-time games record-holder with a 10-point victory over West Coast at the MCG on Saturday.
But Elliott's left knee injury, coupled with setbacks for Darcy Moore (hamstring) and Will Hayes (dislocated shoulder), took some shine off the celebration.
There is also a watch on star midfielder Nick Daicos, who was sent for scans on Sunday after having a foot stomped on.
Elliott, 33, was the Magpies' leading goal-kicker last year with 60 majors and scored three against West Coast, taking his tally to 17 in 11 games this season.
But the 33-year-old, who is contracted for next year, will spend the rest of the 2026 campaign on the sidelines as Collingwood (5-5-1) fight for a finals spot.
Elliott landed awkwardly on his left leg in the dying stages against West Coast and immediately grabbed for the knee as he crumpled to the turf, before he was taken from the field on a stretcher.
"We are all incredibly disappointed for Jamie," Magpies football manager Charlie Gardiner said in a statement on Sunday.
"Scans this morning confirmed that he has ruptured his ACL and has also sustained some bone bruising in the knee.Â
"Jamie has endured a number of significant injury setbacks across his career and for him to face this latest setback is unfortunate for him and his family and for us as a club.
"He's a much loved and respected leader at our club and we're all feeling for him.
"We will miss his on-field presence this year, but he will no doubt continue to play an important role across the club during his recovery."
Daicos was best afield against West Coast with 34 disposals and three crucial goals, but is in doubt for Collingwood's clash with the Western Bulldogs at Marvel Stadium on Saturday night.
"I just had, I think, my foot stomped on," Daicos told the Seven Network on Sunday.
"So just making sure there's nothing wrong with it, but it feels good, so (it's) just precautionary."
Pies captain Moore and young forward Hayes require further assessment before their return-to-play plans are confirmed.
Moore has a "moderate grade" hamstring injury and faces further time on the sidelines after managing just four games this season because of soft-tissue injuries.
"It's definitely frustrating," Moore told the Seven Network on Sunday.
"You put a lot of work in, and you probably put in three times as much work when you're injured than when you're healthy."
Moore's next match will be his 200th AFL appearance.
Meanwhile, Carlton utility Matt Carroll will have surgery after scans confirmed he ruptured an anterior cruciate ligament in the Blues' big win over Port Adelaide.
"Matt had been in excellent form this season and was coming off a strong performance the week prior, so clearly this is a disappointing setback for him," Carlton football manager Chris Davies said.
"While we're all disappointed for Matt, we know how resilient he is, which will serve him well throughout his recovery."
