Mizoram Police FC had taken an early lead through Lalfakawma who scored after being set up by Lalramtharmawia.
Chawnpui FC responded right at the start of the second period with Jerry F. Zonunsanga scoring the equaliser.
A much improved Chawnpui FC looked bright as the match wore on while Mizoram Police FC missed chances to retake the lead with Lalbiakhlua and Lalfakzuala coming close.
And it was Chawnpui FC who struck with only three minutes left as Lalruatfela finished off a ball from K. Roluahpuia.
The win lifts Chawnpui FC into fifth place, a point behind their opponents.
MATCH STATS
Chawnpui FC 2-1 Mizoram Police FC
(C: Jerry F. Zonunsanga 47′, Lalruatfela 87′; M: Lalfakawma 19′)
MoM: Jerry F. Zonunsanga (Chawnpui FC)