Striker Riga Mustapha gave Pune FC the lead with a penalty before Milkan Mrdakovic pulled one back for the hosts.
In the second half, Closa Gonzales gave Tampines the lead. Mrdakovic further extended it in the 69th minute.
With this loss, Pune FC slipped down to fourth place in the group behind leaders Kitchee SC (7 points), Nay Pyi Taw FC (4 points) and Tampines Rovers (3 points).
Stopwatch: Tampines Rovers FC 3 (M Mrdakovic 38' 69', C Gonzales 61') bt Pune FC (R Mustapha 15') 1