Kristoff sprinted to victory along the Muscat corniche, a hair ahead of France's Bryan Coquard and Giamco Nizzolo of Italy in a little over three hours on the 135.5km course.
And the bunch sprint finish meant overnight leader Lutsenko held on to claim overall victory with Astana team-mate Miguel Moreno of Colombia second and Spaniard Gorka Insausti third.
Stage six results:
Alexander Kristoff (NOR/Emirates) 3hrs, 11min, 29sec, 2. Bryan Coquard (FRA/VC) same time, 3. Giacomo Nizzolo (ITA/Trek-Segafredo) s.t., 4. Magnus Cort Nielsen (DEN/Astana) s.t., 5. Nathan Haas (AUS/Katusha) s.t., 6. Davide Martinelli (ITA/Quick-Step) s.t., 7. Amaury Capiot (BEL/Vlaanderen-Baloise), s.t., 8. Greg Van Avermaet (BEL/BMC) s.t., 9. Benjamin Declercq (BEL/Vlaanderen-Baloise) s.t., 10. Floris Gerts (NED/Roomp.