Mooy has an infection in the deep cut in his knee he suffered in the Terriers’ vital victory over Bournemouth last weekend.
The Australian, who has been one of Huddersfield’s key figures this season, will be sidelined for both Sunday’s (AEDT) FA Cup tie against Manchester United and next week’s Premier League fixture against West Brom, and is also in doubt for the March 4 game against Tottenham.
Mooy was dynamic in the 4-1 win against Bournemouth, setting up two goals, before being stretchered off.
Wagner hopes the enforced layoff for the midfielder will allow him to get more rest and be revitalised both physically and mentally as the Yorkshire outfit seek to avoid relegation over the final three months of the season.
“You always try to take the positives out of situations as a manager,” Wagner told The World Game.
“This could be positive that Aaron has to rest. He can make cardiovascular, upper body training because he only has to be careful with the area where he has the stitches.
“He will be ready to kick a ball again after these two weeks. Yes you always try to get the positives, even if I could make the decision to have him fit with us.
“What we tried to do in the last four weeks to be totally honest where we gave him some times off from training.
“Where we left him out of the squad or he came from the bench, so we tried to deal with this situation where he played so many games to get him back to his freshness. Especially his mental freshness.
“I think Bournemouth was a big step for him. He was back to his best and now there is a short, two-week break that we have to accept and hopefully he can continue on the level he has shown against Bournemouth."
There were fears that Mooy may have suffered a ligament damage in the collision in the Cherries game, but Wagner said the 27-year-old should be fit to play again in two to three weeks.
"It’s only a cut but unfortunately there was an infection when he got his stitches,” he said.
“This means there is a slight setback. But nothing serious, so he will miss the next two games for sure. Maybe Tottenham as well, but then he will be back. So it isn’t something where ligaments or muscles are damaged.”
Mooy has had a heavy workload since he joined Huddersfield from Melbourne City in June 2016. The central midfielder has made 80 appearances for his club, along with countless internationals for the Socceroos, in the past 20 months.
"I feel always sad if my players are injured,” Wagner said.
“Especially Aaron who played at a very high level against Bournmeouth, back to his best. It’s very unlucky for him.
“But he will be come back fresh – mentally and physically as well – in two weeks and he will help us. We have options on this position even if we never want to lose Aaron or any of our other players."