Arthur Levinson, chairman of the biotech company Genentech Inc. and a Google board member since April 2004, resigned effective immediately.
Google CEO Eric Schmidt said Levinson has been "a key part of Google's success these past five years" but offered no specific reason for the departure.
The announcement comes amid scrutiny from government regulators over ties between the companies.
Schmidt stepped down from Apple's board this summer shortly after Google unveiled plans for a personal computer operating system that would compete with Apple's Mac computers. Google also makes software that runs on cell phones, putting it in competition with Apple's iPhone.
The growing overlap in the companies' products had spurred the Federal Trade Commission to look into Schmidt's duel role, concerned about the potential for the two companies to cooperate in a way that would reduce competition. After Schmidt stepped down from Apple's board in August, the FTC said it would continue to examine Levinson's ties at the companies.
Google shares rose $8.03 to $524.28 in morning trading while Apple's stock gained 29 cents to $190.76.