The Project 1t4i rider claimed the 144km stage from Al Awabi to Muscat Heights.
After 20km four riders - Vladimir Isaychev (Katusha), Kevin Hulsmans (Farnese Vini), William Clarke (Champion System) and Alexandre Lemiar (Bridgestone Anchor) - escaped and built a lead of four minutes.
However the Sky and Liquigas teams of leading contenders Mark Cavendish and Peter Sagan respectively fused them with the peloton again inside the final five kilometres.
Nacer Bouhanni (Equipe Cycliste FDJ-BigMat) was third behind Lotto Belisol star Greipel, who won the opening stage. Peter Sagan took stage two.
Briton Cavendish was involved in the final bunch sprint - with 64 riders sharing the winner's time of three hours 23 minutes dead - after failing to contest the first two stages which ended in smaller sprint finishes. He was eighth with Sagan fifth behind Tyler Farrar (Team Garmin-Barracuda) and ahead of Tom Boonen (Omega Pharma-Quickstep) and Andrea Guardini (Farnese Vini-Selle Italia).
Today's victory is Kittel's second of the season: he won a stage earlier this month at the Etoile de Besseges.
Stage four of the six-stage race is from Bidbid to Al Wadi al Kabir on Friday.