Nick Daicos starred as the Magpies celebrated Pendlebury's milestone with a hard-fought 13.14 (92) to 12.10 (82) victory in front of 90,028 fans at the MCG on Saturday.
But Elliott crumpled to the turf under pressure from Eagles defender Tylar Young in a marking contest in the dying stages and was taken off on a stretcher.
"We hope for the best, but we won't know until (he has) scans," Collingwood coach Craig McRae said.
"He's in reasonably good spirits.
"We can't rule anything out but we don't know. I mean, clearly he's injured, we just don't know what extent yet."
Captain Darcy Moore (hamstring) and young forward Will Hayes (shoulder) were also casualties as the Magpies (5-5-1) climbed into a "wildcard" spot with their first win since Anzac Day.
Elliott jumped for a mark in the forward pocket and landed awkwardly on his left knee.
McRae said the 33-year-old was "vulnerable" in the air and could sense the incident unfolding as pressure came from Young, who made contact with his body.
The Magpies' coach didn't want to comment on the contest, but his players took exception to Young's actions and remonstrated with the Eagle.
Most players on the field were involved in a melee that unfolded as Elliott departed.
West Coast coach Andrew McQualter gave Elliott his best wishes and defended Young's role in the incident.
"I looked at it again and I'm certain that Tylar Young did nothing wrong in that marking contest," McQualter said.
"He was competing for the ball, he was in that marking contest, and unfortunately accidents happen in our game.
"I don't what they were remonstrating for. It's disappointing that Jamie got injured, but there's nothing more to it."
Elliott's injury came after Collingwood weathered West Coast's gutsy fightback to ensure a victory to celebrate Pendlebury passing Brent Harvey's all-time games record in his 433rd appearance.
There were nine lead changes in a tight first half before the Magpies kicked 29 points clear in the third term, with Daicos and Elliott (three goals) central figures in what looked like a match-winning burst.
But the plucky Eagles closed to within three points with more than seven minutes left to play, before clutch goals to Dan McStay and Daicos gave the Pies breathing space.
"The game was on a knife's edge into the last quarter, but it wasn't about style points or margins. It was just about honouring Pendles," McRae said.
Daicos was best afield with 34 disposals, seven clearances and three goals, including two brilliant snaps at the Punt Road end.
His third major, when he danced around an opponent and kicked truly, all but sealed the result.
Jack Crisp (28 touches) and Jordan De Goey (26) were also influential, while Pendlebury had 20 disposals and five clearances despite attention from Willem Duursma and Brady Hough.
Pies tall Darcy Cameron was involved in an absorbing ruck battle with Bailey Williams.
West Coast (3-8) were well served by young gun Harley Reid, who made his presence felt with 20 disposals in his 50th game.
Tom McCarthy (30 touches), Hamish Davis (23) and Milan Murdock (22) were all busy, and veteran Elliot Yeo kicked three goals, while Jobe Shanahan and Malakai Champion added two each.
"I'm proud of the way we played," McQualter said.
"We were really competitive on a big stage and we gave ourselves a chance to win.
"We're disappointed we didn't win, because that's what our aim was ... but I thought we saw growth in our players and our team."
