The 29 year-old was getting back to his best form in recent weeks, but finished the win over Newcastle Falcons on Sunday with a broken hand.
Talking to www.gloucesterrugbyclub.com Boer said: "It's called a spiral fracture, and it happened in a tackle. Two of my fingers bent right back and snapped the bone in my hand."
The South African flanker, who has made 20 Zurich Premiership appearances this season, is expecting a recovery period of about a month to six weeks.
"It's very disappointing as the last few months have been tough, and we've just started to get back into a better rhythm. It's incredibly hard to deal with at the moment.
"I'll still be there though with the boys, even if it is only bringing on the water. Everyone still knows how important it is on Saturday.
"It's interesting that the game this weekend is between fifth and sixth. With what's at stake, in terms of Heineken Cup qualification, it's as important as it gets.
"We've haven't played well enough this season, and that shows with our final Premiership standing. This Club needs to be in the Heineken Cup, but there's no use just talking about it, we need to work hard.
"The fact is that is comes down to one game now. We've been in the Heineken Cup for the last few seasons, and we have the motivation to be there next season."
With Boer's absence, director of rugby Nigel Melville and coach Dean Ryan have back-row options with Adam Balding, Peter Buxton, James Forrester, Wales U21 captain James Merriman and Luke Narraway available. Andy Hazell is likely to be ruled out with a head injury.
The Gloucester medical staff will be monitoring Marcel Garvey, Terry Fanolua, Olly Morgan and Phil Vickery, who all missed the semi-final victory, throughout the week to get them ready for Saturday's big game.
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