The Belgian international was given the armband after Robin van Persie was sold to Manchester United.
However, the usually reliable centre-half has allowed a few errors to creep into his game - most notably last weekend at Old Trafford where a poor clearance went straight to the Dutch striker, who fired United into the lead after just three minutes.
In his post-match interviews with French television following the 2-1 defeat, Wenger admitted Vermaelen's error had been "unwelcome", adding "the big defenders don't make this kind of error".
With Andre Santos taken out of the firing line, Vermaelen switched to left-back for the midweek Champions League trip to Schalke, and was unfortunate to deflect a goal-bound effort from Ibrahim Afellay into the net as the Germans fought back for a 2-2 draw.
The 26-year-old is likely to return to the heart of the Gunners' rearguard against Fulham today, probably alongside Per Mertesacker in what had looked a promising partnership.
Wenger admitted Vermaelen needed a morale boost. He said: "Physically Thomas is outstanding, but what has happened to him in recent weeks has affected his confidence.
"You put more pressure on yourself when you are the captain. You want to be the best player in the team.
"However, you cannot be a defender and not make a mistake - but if you make one, then maybe you put a bit more pressure on yourself then because you think 'I am the captain and I cannot afford that'.
"Thomas is a guy who is completely involved in the game - he breathes his football from morning until night, he thinks about it [all the time] and wants to do well."
Wenger maintains Vermaelen is in the side on merit alone.
"If he deserves to play, I play him. Are you captain or not, I think he deserves to play. Thomas can help our stability at the back, that is important," the Arsenal manager said.
"We wanted to win at Schalke, but we could not afford to lose it.
"At least we made the second part of the contract and overall it was important for Thomas to be stable defensively."
Lukas Podolski is another player who appears to be suffering from a dip in confidence.
"In recent games he has been a bit less fresh, he is not used to working at that level of intensity, when you come to England it is a shock," said Wenger.