The Belgian centre-half was, along with goalkeeper Wojciech Szczesny, left out against Bayern Munich in midweek. Despite the importance traditionally placed on the armband within the English game, Wenger insists his skipper must sometimes be prepared to make way for the good of the team.
"In England, it is true the captain is a massive importance," said Wenger. "But (the) one who is a captain and a leader, that shouldn't guarantee you a place in any game."
The Frenchman went on: "For purely sporting reasons, or tactical reasons in the game when you don't think it is the right selection, do you put the player in just because he is captain? That is disrespectful to the guy who doesn't play. For sporting reasons it is not completely justifiable."
Wenger admits getting his central defensive pairing right this season has not proved as straightforward as he had hoped.
Per Mertesacker, so often the target of criticism, and Laurent Koscielny produced a solid display as the team secured a clean sheet in the Allianz Arena, albeit one which in the end was not enough for safe passage into the quarter-finals of the Champions League, with the Gunners ousted on away goals.
Wenger said: "They do well together - it is true, but I can't see any obvious reason why Per and Vermaelen should not do well together.
"Also in some big games, I have played Vermaelen and Koscielny together. You think that should work as well because they are two good football players, one is right-footed and one is left-footed, they compliment each other well. However, sometimes there are mysteries in our game that are difficult to rationalise."
Koscielny was a largely unknown quantity when he signed from Lorient in July 2010, but the 27-year-old is now an established France international and has impressed with some consistent displays, including at full-back, in what has at times been a shaky Arsenal rearguard.
Wenger said: "Koscielny has shown a bit more authority than usual and when he gets into that frame of mind, you can see he has the outstanding qualities. It is something I know he has, but he needs that authority in his game to get his qualities completely out."
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- Laurent Koscielny