Mehdi Kiani opened the scoring for the home side in the 52nd minute before a brace from Artur Geworkyan in the 59th and 71st minutes gave the visitors the win.
The win kept the Uzbek club's hopes of qualifying for the Round of 16 alive while in turn eliminating the Iranians.
The Iranian side came close to scoring early when forward Mehrdad Bayrami connected with midfielder Mohammad Pourrahmatollah's corner but was unfortunate to see his effort rebound off the post.
Tractorsazi were twice more denied by the woodwork in the first-half. Midfielder Saman Narimanjahan's shot took a deflection off a defender to hit the bar, and then Habib Gordani's corner from the left was headed onto the post by defender Hani Hashemi.
The home side took the lead in the 52nd minute through a free-kick from Kiani leaving Nasaf keeper Eldorbek Suyunov well beaten.
In the 59th minutes the visitors equalised when Gervorkyan headed home from close-range after goalkeeper Lak fumbled Kiani's long-range effort.
Nasaf took the lead in the 71st minute when Gervorkyan scored directly from a corner kick from the left.
In the dying seconds the hosts almost grabbed an equaliser when Andranik Teymourian crossed for Edinho to head the ball on goal, but was well saved by Suyunov.