The Vanarama National League champions lost long-serving manager John Askey to Shrewsbury Town last month.
Their search is at an end after Yates, who guided the Moors to safety against the odds last season, said yes to the role at the League Two newboys.
The 48-year-old told the Silkmen's website: “I’m really pleased. It’s happened really quickly but I’m joining a club with momentum and a club that are on the up.
“Everybody at the football club did a fantastic job last season and I just want to carry that on in a very competitive League Two.
“I’m looking forward to working with the players that are here but also bringing in some new faces too. I’ve been very impressed with the Chairman and I’m sure we’re going to work tirelessly to put together a squad that will do well next season.”
Macc chairman Mark Blower said: “I’m delighted to announce Mark as our new manager.
“He has all the attributes that we were looking for and I’m sure he will be a big asset for the club. He has all the credentials to be the perfect man to lead Macclesfield Town on their return to the EFL.”