Substitute striker Thongkhoseim Haokip (36th minute) put Pune FC ahead in the first half before striker Aung Naing (42nd) equalised for the hosts three minutes before the break in the Group H Round 5 encounter at the Paung Laung Stadium.
Pune once again took the lead through medio Arata Izumi (55th) before strikes from Nyien Tazar Win (62nd) and Khaing Htoo (72nd) put Nay Pyi Taw in the lead. However, defender Calum Angus struck in 80th minute to pull Pune FC level.
Pune FC's third draw in the group-stage saw them stay fourth in the table with three points and virtually ended their hopes of progression to the next round.
Coach Mike Snoei made five changes to the lineup handing starts to Arup Debnath, Gurjinder Kumar, Arata Izumi, Prakash Thorat and Mirjan Pavlovic.
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In hot conditions, it was Nay Pyi Taw who took the initiative in the opening exchanges with Pune FC defending deep before finally settling down.
As the hosts started creating chances, Pune FC had custodian Arup to thank as he pulled of a string of saves. First, he acrobatically tipped over striker Carlos Delgado's shot from the left and then denied Zaw Lin from close range.
After half chances at either end, Pune FC finally took the lead in the 36th minute. With the NPT goalkeeper Vanlal Hruai failing to clear a long diagonal ball into the box, Haokip capitalised and headed into an empty net for his first goal on the continental stage.