After Gurpreet Singh had put Punjab in the lead in the 38th minute, Amardip Singh (73rd), Vijay Kumar (74th) and Ranjit Singh (84th) scored one goal each for the winners at the Ambedkar Stadium.
The result helped Punjab finish with nine points at the top of Group B North Zone Qualifiers.
In their earlier matches, Punjab had beaten Himachal Pradesh 2-1 and Jammu and Kashmir 1-0.
The final round of Santosh Trophy will be held in Siliguri later this month.