The absence of Stones is not one of surprise as the defender is still recovering from a hamstring injury that he sustained at the end of last month.
However, both De Bruyne and Laporte, who started in the 1-1 draw against Nottingham Forest in the Premier League on Saturday, are notable omissions from Pep Guardiola's first-team squad.
Along with Stones, De Bruyne and Laporte were absent from team training at the City Football Academy on Tuesday, sparking speculation over their availability for the trip to Germany.
It has now been confirmed by Man City on their official website that the trio have not been selected in Guardiola's squad for the visit to the Red Bull Arena.
The absence of De Bruyne in particular comes as a major blow for the Citizens, with the Belgian playmaker having recorded four goals and 18 assists in 31 games across all competitions so far this season, including three assists in four Champions League group-stage matches.
Laporte, meanwhile, has recently been battling with fellow left-footed defender Nathan Ake for a place in the starting lineup, and has been reduced to seven starts in 14 games since the World Cup break.
In the absence of De Bruyne and Laporte, Guardiola has opted to call up academy duo Alex Robertson and Shea Charles, who both trained with the first-team squad on Tuesday.
Nineteen-year-old midfielder Robertson, who spent a brief spell on loan at Ross County last season, has featured in nine of the last 10 Premier League 2 games for City's Under-21s, scoring four goals including a brace in a 6-0 home win over Arsenal.
Meanwhile, fellow 19-year-old Charles has started in all 19 Premier League 2 matches for the Under-21s so far this season, leading his side out as captain on 16 of those occasions, while the defensive midfielder, who can also operate at centre-back, has four international caps to his name for Northern Ireland.
Elsewhere in Guardiola's squad, January signing Maximo Perrone has been included following his permanent switch from Velez Sarsfield, and the 20-year-old is one of seven central-midfield options along with Robertson, Charles, Ilkay Gundogan, Rodri, Kalvin Phillips and Bernardo Silva.
Ederson, Stefan Ortega and Scott Carson remain the three goalkeeping options for Guardiola, while Kyle Walker, Rico Lewis, Sergio Gomez, Ruben Dias, Manuel Akanji and Ake are the six defenders named in the travelling squad, the latter three are all set to compete for a place at centre-back.
Erling Braut Haaland, who has scored six goals in four games against Leipzig, is also included in the squad along with fellow attackers Julian Alvarez, Jack Grealish, Riyad Mahrez, Phil Foden and Cole Palmer.
Guardiola is set to provide an update on his squad and discuss the challenge that awaits his City side on Wednesday when he faces the media on Tuesday evening.
Manchester City's 22-man Champions League squad in full:
Kyle Walker, Ruben Dias, Kalvin Phillips, Nathan Ake, Ilkay Gundogan, Erling Braut Haaland, Jack Grealish, Rodri, Stefan Ortega, Julian Alvarez, Bernardo Silva, Sergio Gomez, Manuel Akanji, Riyad Mahrez, Ederson, Maximo Perrone, Scott Carson, Phil Foden, Shea Charles, Cole Palmer, Rico Lewis, Alex Robertson