Both teams were tied 1-1 after 70 minutes. Drag-flick specialist V.R. Raghunath struck for Wizards in the 15th minute before Manpreet Singh foxed three defenders to level the match in the 30th minute.
Ashley Jackson, captain Moritz Furste and Bosco del Perez scored for Rhinos in the shoot-out while Nitin Thimmaiah and Edward Ockenden struck for Wizards but in vain.
Rhinos pocketed Rs.75 lakh as prize money.
Delhi Waveriders play Punjab Warriors in the final later Sunday.