The midfielder played 71 minutes in the friendly with Chile before picking up an ankle knock in the 1-0 defeat to Germany four days later, leading to reports suggesting Wenger was “stunned” over the amount of game time given to Wilshere.
"First of all Jack is not injured, that was not the right information," Wenger told Arsenal Player.
"Secondly, I have no problem with the FA, they respected completely what they told me and it was [for Wilshere] to play in one game and be on the bench in the other.
"They did that very well. So there is no misunderstanding there. Exactly [they did what we agreed]."
Wenger added that Wilshere is fit to face Southampton in the Premier League on Saturday with he Gunners' lead at the top of the table now down to two points following their 1-0 defeat to Manchester United at Old Trafford before the international break.
Arsenal - who also saw left-back Kieran Gibbs represent the senior England side over the international break - are expecting to have Theo Walcott available again to tackle his former club this week. The winger has now recovered after spending two months out following minor abdominal surgery.
"Of course you miss a player like Theo Walcott," he said.
"Strikers who get behind the defenders have a very important quality and Theo [Walcott] has that quality.
"Theo had a good start to the season, he scored goals, he provided chances and had assists.
"He can always give you a different option in the game and that is of course vital."
Wenger hopes Walcott can offer support to lone frontman Olivier Giroud and record signing Mesut Ozil, who was rested for Germany's internationals with Italy and then at Wembley following a sickness bug.
"You always want to have a perfect balance (in attack), and if you look at our results our balance was not too bad," he said.
"But Theo has different qualities to other players and I am very pleased that he's back."
Czech midfielder Tomas Rosicky could also feature against the high-flying Saints following his illness, while German forward Lukas Podolski is closing in on a return from a hamstring injury which has sidelined him since the end of August.
"He is doing fitness training on the pitch and starts to do some ball work too," said Wenger. "He still needs two or three weeks before we see him on the pitch for Arsenal."
England midfielder Alex Oxlade-Chamberlain, meanwhile, is "at least one month" away from a return after knee ligament damage, while France Under-21 forward Yaya Sanogo could be fit from his back problem in January.
Wenger feels Les Bleus' remarkable comeback in their World Cup play-off against Ukraine that booked them a place in Brazil next summer can only prove positive for Arsenal trio Laurent Koscielny, Bacary Sagna and Giroud.
"You want overall the players to be in a positive mood, to have a good self-esteem, and that of course comes by thinking you have the job done," Wenger said.
"It is positive for France because it was a big relief and the country needed it.
"There is a lot of unrest between the French national team and the country, since South Africa (at the 2010 World Cup), and that they could turn a situation like that in a positive way will help people to love the national team again."
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