Scans have confirmed the Hungary midfielder ruptured the anterior cruciate ligament in his left knee.
The 33-year-old suffered the injury in the 21st minute of Saturday's FA Cup third-round tie at QPR.
The usual rehab time for the injury is six-to-nine months and Clarke admitted the veteran's absence created a huge hole to fill.
"I'm devastated for Zoltan," said Clarke. "He's a terrific guy and professional and I want to thank him for his contribution this season. It has been invaluable.
"He'll now get our full support during the rehab process. Zoltan has already proven he can come back from this injury once and produce at the highest level and I have no doubts he will do so again."
Gera made 18 appearances this term, having battled back to fitness from a similar injury suffered in November 2011 in time for the start of this season.
He played four times for Hungary in that time and netted four goals for the Baggies in the campaign, with his strikes against Liverpool, QPR, Sunderland and Norwich all helping to secure Premier League wins.