Ralph Keyes' The Quote Verifier says no. Keyes thinks it was just a common proverb.

Stephen Colbert calls quotes like this "truthy". Because it seems like something that Napoleon ought to have said, it has just become something that he's really said.

Proverb or not, there are a couple of previous written examples that are similar. The Comte de Bussy-Rabutin wrote in a letter to the Comte de Limoges in 1677, " Dieu est d'ordinaire pour les gros escadrons contre les petits." God is usually for the big squadrons against the small ones".

Letters of the Count Bussy-Rabutin, v.3 , p.340

Voltaire is usually credited with, " It is said that God is always on the side of the big battlaions", but like a lot of Voltaire attributions this one is not true. There was instead an unpublished diary entry, " God is not on the side of the big battalions but on the side of those who shoot the best.", which is not at all the same.

You might find amusing this blog at the Oxford University Press that goes into some detail how much Voltaire has been misquoted. It seems there might even be T-shirts that say ( in French) "I will defend to my death your right to cite Voltaire incorrectly". This could be expanded to other erroneous one-liners: "You can do anything with a Napoleon quote but sit on it".