The 30-year-old best Bryan Coquard (Vital Concept) and Giacomo Nizzolo (Trek-Segafredo) in a bunch sprint after surviving two punchy climbs that took the sting out of pure sprinters on the route to the Matrah Corniche.
Alexey Lutsenko won the race title ahead of Astana teammate Miguel Angel Lopez, with Gorka Izagirre (Bahrain-Merida) 28 seconds adrift in third.
"I've been up in the mix but haven't managed to fight for the win in these last sprints. The legs have been good but I haven't been able to come into position so I've not been so pleased with that," Kristoff said post-race.
"This morning we had a really good meeting. I've won here before so knew exactly how I wanted it and explained to the guys which moment we needed to move.
"The guys did exactly what we planned, I even had Rui Costa in the lead-out there in the final and he also did a perfect job. I don't think he's done too many lead-outs in his life but when he first did it, it was a good one!"
Australian Nathan Haas snatched the points jersey from the shoulders of Greg Van Avermaet (BMC) on the last day, placing fifth on the stage and overall.
Haas (Katusha-Alpecin) disrupted what was otherwise a clean sweep for Astana, which took out the race title, team classification as well as the best young rider with Lopez.
Kristoff is undertaking a block of training and racing in the Middle East as preparation for the spring classics in which he hopes to return to the form he won both the 2014 Milan-San Remo and 2015 Tour of Flanders with.
The Norwegian opened his season with a winless run at the Dubai Tour earlier this month. However, racing in the all-white kit of European champion, found his legs and a rhythm with new teammates while competing over punchy terrain in and around Muscat.
"Dubai was not so hard racing maybe because it's so flat but here in Oman, it's much harder with the climbs. I think this block of races will be good for me, but we will see how the classics go. If I'm not performing there, maybe it was not good," he said.
"I think I'm going a little bit better in the climbs so that can be useful in the classics but then again the sprints have not been so good as the last years. At least today I managed to show I can still sprint, so I'm very pleased with that."
A five-man break escaped early in the piece, with Frenchman Remi Cavagna (Quick-Step Floors) the last of the lot to be caught some 2.5km from the line.
The sixth stage posed no real threat to overall standings but had some drama.
Adam Blythe (Aqua Blue Sport) was denied a chance to sprint at the finish after being disqualified over an irregular wheel change during the race.
"I just changed my bike. The guys went ahead to get my bike ready for me to change, I had a problem with it beforehand," Blythe said.
"So, went ahead, changed it, I came back, just waited at the back and as the peloton went past I stopped, changed my bike, started to get back on the bunch and the commissaire just said you're out, disqualified. It was something to do with getting the bike prepared in front of the peloton."
Commissaire Jean-Pierre Coppenolle said Aqua Blue Sport didn't follow protocol that deems you must change bikes only from team cars.
"The team manager of Blythe asked me if he may go in front of the bunch to prepare the bike, I say okay, it's easy, he goes out the front and prepares the bike," Coppenolle said.
"But for the changing of bike that must happen behind the bunch and from the car, so he gives the bike but from the ground and with the new rules it's not allowed. The change of bike is always behind the bunch and from the car, and only from the car."
Kristoff will leave Oman for the Abu Dhabi Tour, which is more tailored to pure sprinters over puncheurs, this week.