John Tinker will assume the role for the upcoming third season, according to The Hollywood Reporter.
The network previously confirmed that the series, which stars Jada Pinkett-Smith, would return for ten more episodes.
A spokesperson for TNT refused to elaborate on Mazzara's exit, but commented that the producer currently has several projects in development with Sony Pictures Television.
Tinker previously served as executive producer on both CBS medical drama Chicago Hope and ABC legal drama The Practice.
The second season of Hawthorne concluded on August 24.