The 37-year-old has been at Somerset Park as a player since joining from Falkirk in January 2018 and the former Dundee United and Aberdeen midfielder now replaces Ian McCall in the dug-out following his move to Partick Thistle.
Kerr told the Ayr website: “I am absolutely delighted to have been given this opportunity. This is a fantastic club and right now we have a top group of players and I can’t wait to lead them.”
Chairman Lachlan Cameron said: “It’s been an unsettling few weeks for everyone involved and it’s never an easy process finding a new manager. However, we wanted to do it right and I feel confident in the process and I’m pleased with the result.”