Levinson, who is a corporate director of Apple, had been a Google board member since April 2004.
His resignation comes two months after .
In May, the FTC began an investigation into whether the presence of Schmidt and Levinson on the Google and Apple boards could lessen competition between the two firms.
Under US law, no-one is allowed to serve on the boards of two companies which are direct rivals.
The FTC welcomed Levinson's resignation from Google's board.
John Leibowitz, FTC chairman, said in a statement that both firms and Levinson "should be commended for recognising that overlapping board members between competing companies raise serious anti-trust issues".
Former US vice president Al Gore is the only remaining link between the two Silicon Valley giants. Gore serves on the board of Apple and is an adviser to Google.
The rivalry between the two Silicon Valley giants continues to grow as they encroach on each other's territory.
In July Google revealed it was developing a computer operating system to compete with Apple's own OS and Microsoft's Windows.
Separately, Google's web browser Chrome has also taken a market chunk out of Apple's Safari but, most importantly, Google wants to become a serious rival to Apple's iPhone with its Android phone.
Schmidt, on Levinson's resignation, said: "Art has been a key part of Google's success these past five years, offering unvarnished advice and vital counsel on every big issue and opportunity Google has faced.
"Though he leaves as a member of our board, Art will always have a special place at Google."
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