The former Barcelona man will begin work at the Etihad Stadium within the next fortnight in a move that sees Brian Marwood become managing director of the City Football Academy.
It is believed that City's new chief executive Ferran Soriano, who worked with Begiristain at Barca, was instrumental in bringing him to the club.
"I'm pleased to have such an opportunity," said Begiristain.
"I look forward to working with Brian Marwood, Roberto Mancini and Ferran Soriano in building a team and philosophy which will serve City well in the near and long-term future."
Begiristain left Barca in 2010.