The initiative began in the wake of the terrorist attack at Manchester Arena after an Ariana Grande concert on Monday and is designed to assist the families and dependents of the 22 people who died and the 64 who were injured.
The fund had reached £2m by Wednesday and the donation from City and United increases that total to beyond £3m.
"We have all been humbled by the strength and solidarity shown by the people of Manchester in the days since the attack," City chairman Khaldoon Al Mubarak said.
"The hope of both our clubs is that our donation will go some small way to alleviate the daunting challenges faced by those directly affected and that our acting together will serve as a symbol to the world of the unbreakable strength of the spirit of Manchester."
Ed Woodward, executive chairman of United, said: "The barbarism of Monday evening's attack has shocked everyone. Our clubs are right at the heart of our local communities in Manchester and it is right that we present a unified response to this tragedy.
"The money will help, of course but the work of the two clubs and their respective foundation and community scheme can build on the fantastic spirit that Mancunians have shown in the immediate aftermath."