Striker Wayne Rooney scored his first England goal for a year in the 37th minute and his side looked to have gained a morale-boosting victory until Van der Vaart's 86th minute strike at the Amsterdam Arena.
The draw will leave a bitter taste for England, who were coming off a dismal run in Euro 2008 qualifying, having lost 2-0 in Croatia and drawn 0-0 at home to Macedonia last month.
Their skilful Dutch hosts enjoyed plenty of possession but lacked the usual bite provided up front during their own qualifying campaign by striker Robin van Persie, who was absent here due to impending fatherhood.