Dana Stubblefield -- Wife Filed for Divorce ... After Alleged Rape

Dana Stubblefield was married at the time of his sexual encounter with a babysitter -- but his wife has since filed for divorce ... TMZ Sports has learned.

Terri Stubblefield filed divorce docs in Santa Clara County family court on February 29th -- seeking to end her nearly 7-year marriage to the former NFL star. She cites irreconcilable differences.

According to the docs, filed by Terri's lawyer John Conway, Terri lists the date of separation as Feb. 17th.

The incident with Dana and the babysitter went down in April 2015 ... but we're told he wasn't contacted by investigators until March 2016.

The couple has 2 children together -- a 1-year-old and a 4-year-old.