The former City captain had been due to feature in the star-studded charity match that will see a City legends team face an all-star XI of former Premier League players to raise money for his homelessness charity Tackle4MCR.
Kompany left the Premier League champions in May to become player-manager at Anderlecht and, much like the latter half of his City career, was hit by a muscle injury in defeat to Genk last month.
"Unfortunately I can't start or even play. I have a slight hamstring injury and can't risk it. It's typical me," said Kompany.
However, the Belgian international played down his frustration at missing out with the most important goal raising funds for charity.
Current City stars David Silva and Sergio Aguero will line-up alongside the likes of Mario Balotelli in a team managed by Pep Guardiola.
They will face an all-star side littered with former Manchester United greats like Edwin van der Sar, Gary Neville, Paul Scholes and Ryan Giggs, but also boasting Thierry Henry and Robin van Persie in attack.
"We are specifically dealing with homelessness in Greater Manchester. You can't have a successful project without Manchester United involved. We have our differences - that is clear - but if we can get together for these sort of events the city is stronger."
City failed to replace Kompany in the summer transfer window and are now short at centre-back with Aymeric Laporte facing a lengthy spell out injured.
However, Kompany is confident that Guardiola will ensure Laporte's absence is not as costly as it seems over the next few months.
"By losing Laporte you lose a big player. You need big players in the bigger games but the key strength of this Manchester City team is relying more on the system than the individuals.
"I don't see City weakening. Pep is way too aware of this danger to let it happen."