Arsenal are currently top of Group H, level on nine points with Shakhtar Donetsk but ahead on their head-to-head record, while Braga are three points behind having secured back-to-back victories against Partizan Belgrade.
A defeat could therefore give Arsenal problems going into their final game against Partizan Belgrade but, following the 3-2 defeat at home to Tottenham on Saturday, Wenger believes some of his players need to be rested.
"I left Clichy behind because he has a small back problem and we will take the opportunity to clear that out," he told a press conference on Monday. "Arshavin [is not in the squad] because I want to give him a rest, he has played every single game recently and played for Russia on Tuesday night.
"Van Persie [will not travel] so he can improve his fitness because he is back in the squad but is not 100% fit at the moment - I mean his physical condition to fight in a top-level game.
"I think that [working hard on the training ground] is what he needs at the moment. If I take him to Braga and he is not 100% and is on the bench and doesn't come on then it is a waste of time and for three days, so I leave him behind and he will take the opportunity to work."
Captain Cesc Fabregas is expected to feature in the game and Wenger said the hamstring injury that has caused problems since the World Cup is now improving.
"It is getting better," he said. "He was out for a while and had a recurrence of his hamstring problem, then it gets in your head.
"When it gets in your head, it is difficult to play free of your mind. I feel it is getting better in every match - from game to game he becomes stronger.
"On Saturday against Tottenham, he has created three great goal chances, so we are getting back to the normal Cesc.
"Sometimes after the game he has a little recurrence, but at the moment I do not want to take a massive gamble.
"We cannot afford to lose him, so I check every morning of the game how he is and we monitor him quite well, but it is on the way up."