Mayer, 31, and Aniston, 40, have been dating on and off since May 2008. According to People, the duo broke up when Aniston returned home from Europe, where she was promoting her movie Marley & Me.
"They had some disagreements and decided to not continue to see each other," said a source. "Jen is moving on with her life like she always does. She seems happy."
Representatives for the two stars have not commented on the reports.
Mayer broke up with Aniston in August 2008, announcing the news outside a New York gym. However, the couple have been spotted together frequently since and recently attended the 2009 Oscars together.