Khan, of Petroleum Sports Promotion Board who had won the crown beating Kamal Chawla in the last nationals at Chandigarh, outsmarted his rival despite suffering a wobble midway after taking a 2-0 lead in the best-of-seven encounter.
Siddharth Parikh of Railways also struggled to overcome another qualifier Viren Sharma of MP in the decider after leading 2-0 and 3-2 in Group L.
In other ties that went the distance, India junior snooker champion Laxman Rawat of Delhi rallied to beat qualifier R Girish of Railways 4-3 after leading 2-0 and 3-2 in Group N, while Dr I H Manudev rallied from a 1-3 deficit to beat Mundir Sherazi 4-3 in an all-Karnataka Group J thriller.
In a significant win, Pune-based Yogesh Sharma upset state rival and junior snooker champion Jaiveer Dhingra 4-2 in Group K. Dhingra initiated a late challenge after trailing 0-3.
In women's section, former national snooker champion Anuja Thakur-Chandra of PSPB and Neena Praveen of Tamil Nadu registered contrasting wins in their opening group matches.
Anuja warmed up for sterner tests ahead when she rallied from the loss of a tight opening frame to beat national 9-Ball Pool champion Suniti Damani of West Bengal 3-1 in the best-of-five Group D tie.
The other winner in the group was Anuja