Sir Bradley Wiggins finished fifth overall in the Giro del Trentino after his bike suffered mechanical problems.
The Team Sky rider had to change bikes midway through the finishing climb of the fourth and final day of the Giro d'Italia warm-up.
The three-week Giro d'Italia starts on 4 May in Naples.
Italian Nibali, who finished third in last year's Tour de France, completed the 167-km leg from Arco to Sega di Ala ahead of second-placed Italian Mauro Santambrogio and Polish rider Przemyslaw Niemiec.
Overall, Nibali finished 22 seconds ahead of Santambrogio and French rider Maxime Bouet, who started the fourth day with more than a three-minute lead, finished third overall, 55 seconds back.
Wiggins began the final day in third position overall and was in the lead group on the Sega di Ala ascent with 5km remaining when his bike failed him.
He fought back to finish the fifth and final stage in ninth place.
Final overall standings:
1. Vincenzo Nibali (Italy, Astana) 17:49:11"
2. Mauro Santambrogio (Italy, Vini Fantini-Selle Italia) +0:22"
3. Maxime Bouet (France, AG2R La Mondiale) +0:55"
4. Fabio Aru (Italy, Astana) +1:16"
5. Bradley Wiggins (GB, Sky) +1:40"
6. Przemyslaw Niemiec (Poland, Lampre) +1:45"
7. Stefano Pirazzi (Italy, Bardiani Valvole) +2:15"
8. Cadel Evans (Australia, BMC) +2:18"
9. Stefano Locatelli (Italy, Bardiani Valvole) +3:05"
10. Pierre Rolland (France, Europcar) +3:22"