Kristoff (Katusha) casually raised his arms after winning the bunch sprint from Giant-Alpecin teammates Zico Waeytens and Soren Kragh Andersen at the end of a less than straightforward lead-out.
Nibali claimed the tour title ahead of Romain Bardet (AG2R) and teammate Jakob Fuglsang in what was an early boost of confidence ahead of major targets including a Giro d’Italia title tilt.
The Italian was the best climber in Oman with a showing on Green Mountain pivotal to his triumph.
“I’m happy with this win, especially seeing as I came very close to winning here before only to lose this race by a second (in 2012),” he said.
“It’s clear that it’s been a good start to the season and now there’s time to recover a bit before the important races in Europe. It was very important for me to try to get a win straightaway. There are important races coming up in the weeks to come.”
Kristoff’s Katusha was separated when an increase of pace over a climb in the final lap of a finishing circuit in Matrah Corniche split the peloton.
The 28-year-old lost teammates, including Michael Morkov, but recovered with Marco Haller again doing a massive turn to make up ground and deliver Kristoff and his chief pilot, Jacopo Guarnieri into position.
“At two kilometres to go we were actually not in the first group, there was a small gap and we were in the second,” Kristoff said. “But Marco took us from two kilometres to 500m, so he did a really good pull again, like the last sprint in Oman here, and from 500m Jacopo sped up and delivered me perfectly.
“It was a good lead-out with two guys. I’m happy with how we went the last lap because we could have panicked but we stayed calm and took them from behind a few hundred metres.”
The victory is Kristoff’s fifth of the season and second in Oman following three wins at the preceding Tour of Qatar. His Katusha train at both races was impressive either in being insurmountable or quick thinking.
The action came at the end of the 130.5km run from The Wave Muscat where riders on the last day took advantage of coffee chain stores by the start line.
After a fast and aggressive start where attacks where nullified through narrow, suburban streets with plenty of road furniture, a seven-man group including Sebastien Minard (AG2R), Gregor Muhlberger (Bora-Argon 18), Gianni Meersman (Etixx-QuickStep), Jesper Asselman (Roompot Oranje Peloton), Pieter van Speybrouck (Topsport Vlaanderen-Baloise), Daniel Eaton (UnitedHealthcare) and Jaroslaw Marycz (CCC Sprandi Polkowice) escaped after about 20km.
The group led the race for much of the day but was whittled down to just two riders within the final of three laps of the finishing circuit where a large bunch arrived at the finish.
Kenny Dehaes (Wanty-Groupe Gobert) arrived more than nine minutes down for last place after a lonely but notably determined effort to finish the race.
Kristoff will return to his home in Norway before the classics in further preparation for a busy schedule set to include a Tour of Flanders title defence.
Australian Brendan Canty (Drapac) claimed the best young rider’s jersey. The rookie pro retained it after an impressive move on Green Mountain earlier in the tour. Dimension Data took out the team, points and most aggressive classifications.