The away side came into the game five points adrift at the bottom of the table and without Elvis Manu, who failed to have his wrongly awarded red card rescinded by the KNVB.
For Willem II, the match was the chance to all but seal their place in the Eredivisie next season.
The home side had an early Thom Haye goal ruled out for offside, but it was Go Ahead Eagles who had the better of the first half. Kostas Lamprou denied Marcel Ritzmaier, Sam Hendriks and Jarchinio Antonia, while Xandro Schenk put a header wide.
At half-time, Willem II brought on Fran Sol and it was the Spaniard who finally opened the scoring on 72 minutes with a close range header. Another substitute, Jari Schuurman, then sealed the win for the home side with a well-timed volley in the box.
Go Ahead Eagles now must find at least six points from their last three games to stop their relegation, while Willem II move 10th.
