The Slovak rider prevailed at the end of the 190km route from Nakhal Fort to Wadi Dayqah Dam, the longest stage of the race.
The Cannondale rider beat Belgian Greg van Avermaet (BMC) and Tony Gallopin (RadioShack) to the line with Alberto Contador in fourth place.
Sagan leads Gallopin by 16 seconds on the general classification.
Dutchman Bobbie Traksel made another early break along with Yusuke Hatanaka of Japan, Italian Christian Delle Stelle and David Boucher of France. And they built up a maximum lead of 8:30.
The only serious climb of note was the short and sharp Bousher Alamrat where Bardiani Valvole's Delle Stelle left his fellow escapees.
Hatanaka regained contact but the peloton eventually regained contact with 18km to go.
Tom Boonen, Team Sky’s Bradley Wiggins and Matthew Goss were amongst those dropped on the run-in to the line where Sagan had the speed to record the 49th win of his brief career.
Thursday’s mountainous stage sees the riders negotiate the 152.5km route from Al Saltiyah in Samail to Jabal Al Akhdhar.