Germany head coach Low announced this week that Thomas Muller, Jerome Boateng and Mats Hummels will no longer be considered for international duty as he attempts to usher in a new generation of talent.
Bayern released a statement hitting out at the timing of Low's decision, with a Bundesliga game against Wolfsburg on Saturday followed by next week's Champions League last-16 second leg at the Allianz Arena.
And Wagner, a Bundesliga champion with Bayern for the second time last season before leaving for Tianjin Teda, thinks Niko Kovac's side will take out their frustrations on Liverpool.
"I'm sorry for the guys. All three are great players, world champions and great people - each in their own way," he told Bild.
"But I'm sure it'll be a positive for Bayern's season. Mats, Jerome and Thomas will now want to show everyone they are still at the absolute highest level.
"With this anger, the boys will blow Liverpool away in Munich."
Bayern held Jurgen Klopp's side to a 0-0 draw at Anfield in the first leg.
They will first look to keep pace with Borussia Dortmund at the top of the Bundesliga when they take on Wolfsburg this weekend.
The German champions are riding the crest of a wave at the moment, picking up five wins from their last six matches across all competitions.
Dortmund are now only top of the domestic table on goal difference, having surrendered a six-point lead over their arch-rivals in recent weeks.
Liverpool, meanwhile, will warm up for their trip to the Allianz Arena with a tough home game against Burnley in the Premier League on Sunday.