The Belgian centre-half was, along with goalkeeper Wojciech Szczesny, left out against Bayern Munich in midweek, but could return for Saturday's trip to Swansea.
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, whose previous Arsenal skippers were Tony Adams, Patrick Vieira, Thierry Henry, William Gallas, Cesc Fabregas and most recently Robin van Persie.
"But (the) one who is a captain and a leader, that shouldn't guarantee you a place in any game.
"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."
Lukasz Fabianski, meanwhile, did his prospects of retaining the goalkeeper's jersey no harm with a solid performance against Bayern, making some telling saves in what was a first senior Arsenal appearance in more than a year.
Wenger feels the Poland international has come full circle since a string of errors - including a howler against Chelsea which gifted Didier Drogba the winning goal in the 2009 FA Cup semi-final at Wembley on his 24th birthday - saw him labelled 'Flappy Handski' by some supporters.
"He has top quality, Fabianski. He has gone through difficult times, but he faced it and handled it and he did something about it," said Wenger.
"He lacked a bit confidence, suffered a bit under pressure, but let us not forget that to mature helps as well, that is one of the advantages of ageing.
"I believe more as well that technical approach is very important, that you manage to focus on what is important in your game."
Fabianski, signed from Legia Warsaw in May 2007, was hampered by ankle and knee problems injury earlier in the season, which saw Italian Vito Mannone emerge as understudy to Szczesny, playing a dozen first-team games including in the Champions League.
There had been suggestions Fabianski, who was also number two under Manuel Almunia, would be allowed out on loan.
Wenger understands it is a difficult spell in the player's career.
"The problem for Fabianski is that he is 27, not 19. He is at an age where a goalkeeper needs to play, he wants to play," said Wenger.
"Every guy wants to play, but they want to play in big clubs as well where there is a lot of competition."
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