The 31-year-old Team Dimension Data rider completed the 189km course, which runs entirely in the desert, in four hours 37 minutes six seconds.
Germany's Andre Greipel and Italy's Niccolo Bonifazio completed the top three, while Spaniard Alberto Contador suffered a crash 4km from home.
Friday's 153km-stage takes the riders from Almaryah Island to Big Flag.
Stage one result:
1. Mark Cavendish (GB/Dimension Data) 4hrs 37mins 6secs
2. Andre Greipel (Ger/Lotto)             Same time
3. Niccolo Bonifazio (Ita/Bahrain)     Same time
4. Simone Consonni (Ita/UAE Team Emirates)          Same time
5. Elia Viviani (Ita/Team Sky)               Same time
6. Roger Kluge (Ger/Orica)             Same time
Britain's Mark Cavendish won the first stage of the Abu Dhabi Tour after a sprint to the line.