A haggard looking Cavendish finishes second to a lively Andre Greipel in an earlier stage.
Sky rider Mark Cavendish won the Ster ZLM Toer at the end of the fourth and final stage on Sunday. The Briton finished in 16hr 11min 55sec, eight seconds ahead of Dutch rider Lars Boom, with Belgian Juergen Roelandts in third at 14sec.
World champion Cavendish, who won three stages on last month's Giro d'Italia but missed out on his goal of the sprinters' red jersey by just a point, competed here with an eye on his next two objectives - the Tour de France and the Olympic Games.
Isle of Man sprinter Cavendish has won a total of 20 stages at the Tour de France and last year brought home the sprinters' green jersey for the first time.
He will aim for more of the same in the three-week epic, from June 30-July 22, before turning his attention to the men's Olympic road race on July 28.
1. Marcel Kittel (GER/Argos) 3hr 35min 54sec, 2. Mark Renshaw (AUS) same time, 3. Juergen Roelandts (BEL) s.t., 4. Raymond Kreder (NED) s.t., 5. Alexander Porsev (RUS) s.t.
1. Mark Cavendish (GBR/Sky) 16hr 11min 55sec, 2. Lars Boom (NED) at 8sec, 3. Juergen Roelandts (BEL) 14, 4. Juan Antonio Flecha (ESP) 15, 5. Giacomo Nizzolo (ITA) 18