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' 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 Premier League clash on Saturday, 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."
Albion are challenging for a European spot but Clarke will not contemplate such targets until the 40 point safety mark has been achieved.
He said: "Albion want to be challenging in the top half of the table more often than not.
"Albion have built well over the last two or three years and we are in a strong position just now.
"Rather than us thinking about the fact we are playing teams down the bottom of the league, it's more for us to try and keep our noses in front of the teams that are trying to catch us up.
"Is Europe a possibility? Yes, I think I should make Europe at the end of the season for a holiday!
"Listen, we just keep working and working. The first target was 40 points. We haven't reached that yet.
"Maybe when we reach 40 points, I'll answer questions on Europe."
Clarke wants Albion to recapture the fluency that was the trademark of their performances during the early part of the campaign.
He said: "I think the month of December was a little bit up and down. We had good and bad spells.
"I think it is important we try and get back to a similar rhythm to what we had earlier in the season. I think we've lost that. We are not quite as fluent as we were.
"But we've shown in games in December, like against West Ham, Norwich and QPR, that we can go and dig out results without playing particularly well.
"I think at this stage of the season, sometimes that's what you have to do. At the moment, we have to dig out some results, keep pushing up the table, getting the points tally to where we want it.
"Some injuries to key players has disrupted us, we are hopeful those players will soon be back and, once we get them back, we can look forward to more fluency and some better performances."
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