He filed the papers last Friday, Extra first reported.
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Penn, 48, initially filed for divorce in December 2007, but his petition was later dismissed. Three days later, Wright Penn, 43, filed her own paperwork.
But in April 2008, the couple's divorce petition was dismissed at their request.
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They attended February's Academy Awards, where Penn won his second Best Actor Oscar for his role as gay rights activist Harvey Milk.
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He did not thank Wright Penn -- with whom he has two children, Dylan, 18, and Hopper Jack, 15 -- while accepting his award.
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After the show, he told Oprah Winfrey that his gratitude for his wife was "implicit."
"I wanted to keep things focused on the professional team around this movie," he explained. "Because with Robin comes my mother and my son and my daughter, and half of them will punish me if I mention them."
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