Wonder, 62, real name Stevland Morris, cited irreconcilable differences and listed the couple's date of separation as October 2009.
The papers obtained by Reuters showed that the "Superstition" singer was asking for joint custody of the couple's two boys, 10-year-old Kailand and seven-year-old Mandla.
The singer, who has been blind from birth, signed the papers using two fingerprints and agreed to pay spousal and child support. He also requested that all his earnings after the separation were kept separate from the couple's assets.
Wonder and Millard Morris were married in September 2001. The singer was previously married to Motown singer Syreeta Wright from 1970 to 1972, and has had several relationships since, from which he has seven children.
Wonder rose to fame as a child musical prodigy in the 1960s and has since won 22 Grammy awards and a Grammy lifetime achievement award for his work.