Arsenal face fierce rivals Tottenham at the Emirates Stadium on Saturday with a shortage of defenders.
Minor problems saw Mertesacker and Gibbs miss the cup clash with Southampton, forcing Wenger to name an inexperienced defence that included 19-year-olds Hector Bellerin and Isaac Hayden.
Nacho Monreal's continued absence meant Calum Chambers was the only regular starter named by the Frenchman but the youngster had only made seven previous appearances since joining from Southampton.
Arsenal's young side were beaten 2-1 by Ronald Koeman's men but Wenger said he is confident his experienced duo of Mertesacker and Gibbs will be fit to face Spurs on Saturday.
"They will be alright," Wenger said. "We are a bit short, yes, because of the injuries we have.
"You sit there and think Gibbs had a little hamstring problem and we could not play him.
"Mertesacker is a bit on the edge, and then we have no choice."
Wenger's options at the back were reduced on Monday when France international Mathieu Debuchy was ruled out for three months following surgery on his left ankle.
