The soul singer tops the bill for the event's final night on September 9.
The star joins New Order - who are headlining on Saturday - as well as one more act, who is to be confirmed in the coming weeks.
Other names already on the bill for this year's event include Friendly Fires, The xx, Azealia Banks, Emeli Sandé, Charli XCX and Major Lazer.
Wonder - who headlined Glastonbury in 2010 - released his 23rd studio album A Time to Love in 2005, which peaked in the top five on the Billboard chart.
Bestival takes place between September 6 and September 9 at Robin Hill Park, Isle of White. Tickets, priced between £120 and £180, are on sale now.
Last year's festival included Bjork, Metronomy, The Cure and Katy B.
Watch Stevie Wonder perform 'Superstition' below: