The Italian defender is set for surgery on a hamstring problem next week that will rule him out of action for the remainder of the campaign.
Pascali was forced out of last weekend's 3-0 win over Hearts before discovering the severity of the injury.
Boss Kenny Shiels said: "He's out for the season and it's a big blow for us.
"We really feel for him because he is such a good person around the players and he's a good captain.
"We are going to miss him off the pitch and on the pitch.
"It's really difficult to take in, the way we have been hit. We have taken a big hit since January.
"The boys have stepped up and we need them to step up again. It's a big loss."
Pascali endured a similar setback this time last year when he suffered a broken leg - a month before Kilmarnock lifted the Scottish Communities League Cup.
Shiels added: "He had the injury going into last season's final and we've got a cup quarter-final this time so it's going to be difficult for him but he's a strong boy."