Gera will be sidelined for the rest of the campaign after suffering a second serious ligament setback in just over 12 months.
But Clarke feels Thomas is the natural replacement after proving his fitness during a loan spell at Leeds following an injury-hit start to the season.
Thomas's current deal expires in the summer but the former Charlton player has made it clear he would like to remain at the Hawthorns.
Clarke, whose side visit Reading for a Barclays Premier League clash, said: "Jerome Thomas is the one that can cover for Zoltan because we didn't have Jerome in the first half of the season.
"He was always injured. Then when he got himself fit and was in the squad, the team was in a great place and he had no prospect of playing matches.
"He went out to Leeds to get match fitness, which he did, and he's come back to us and the timing couldn't be better."
When asked about Thomas earning a new deal, Clarke said: "It's a great chance for him. He'll get chances to play.
"He'll be in and around the squad and the team and, what he has to do, is show the form he's shown in previous seasons because he's been a good servant for Albion.
"We look forward to some really good performances from him in the second half of the season."