Mertesacker enjoyed arguably his finest display for Arsenal in last weekend's 1-1 draw against Manchester City, but was left out in favour of the returning Thomas Vermaelen for the 2-1 home defeat against Chelsea.
Wenger believes that he is open to criticism for the decision but stands by his choice.
He told the club's official website: "That is a decision which was based on the opposition we played.
"You can say it was a wrong one maybe, but I believe [that statement] is lowering the quality of the players who played, they are internationals.
"If you do not play Laurent Koscielny or Vermaelen and cannot win the game, you will ask me the same question. Nobody can play all the games, it is simple."
Defeat to the Blues cost Arsenal their unbeaten Premier League record, with the Gunners standing in 7th place in the table after six matches.