The Central Asian team took the lead when Vadim Harchenko's cross in the box found an unmarked Zemlianuhin, whose powerful right-footer crashed into the net.
Kyrgyzstan doubled the lead few seconds before the breather after Amirov made a solo run into the box and shot past goalkeeper Asanka Viraj.
Eight minutes into the second half, Sri Lankan captain Weerasinghe headed in from a flag-kick to reduce the margin.
Kyrgyzstan stepped up the accelerator in the last 15 minutes and Harchenko's pin-point cross found Murzaev, who nodded past Viraj. Five minutes later, Usanov dodged past the Sri Lankan defenders and slotted home.