The LA Galaxy player filed divorce papers on Tuesday at the Los Angeles Superior Court.
“We remain the closest of friends and will always be important parts of each other’s lives,” the pair said in a joint statement.
The pair married on New Year’s Eve in 2006 in Santa Barbara but split in October 2009.
Rumors about a possible reconciliation appeared during the World Cup in June after the two attended several events together.
Days later, a cheating scandal broke out after rumors circulated that Donovan fathered a love child in the UK while playing on loan for the English Premiere League’s Everton club in the winter of 2009.
Donovan denied the allegations, telling E! News, “I will not be a dad any time soon, which is good news for me.”
28-year-old Donovan cited irreconcilable differences and is seeking spousal support, as well as attorney fees. The two have no children together.