Chhetri, who scored his 54th goal in his 94th match, led from the front throughout the match. Playing behind the lone striker Jeje, he was in the thick of things, at times falling back deep to help the defenders, setting up his team-mates and also taking shots on his own.
With the win, India sat atop the group with six points -- from two wins -- ahead of Kyrgyzstan and Myanmar who both have three points from two matches. Macau is yet to open an account from their two matches.
All the four teams will play home and away matches and the two top sides will qualify for the 2019 AFC Asian Cup to be held in the United Arab Emirates.
The hosts, who had beaten Myanmar 1-0 in their first match of the qualifiers, notched up their seventh official international match on the trot.
Kyrgyzstan had better ball possession and more attack but they found wanting in their finishing. The Indian back-four of Sandesh Jhingan, Anas Edathodika, Pritam Kotal and Narayan Das were also superb in defending.
The visiting side was denied by the upright in the second half while Indian goalkeeper Gurpreet Singh Sandhu made at least three brilliant saves to ensure that the hosts walked away with all three points.
Kyrgyzstan, who are ranked at 132 as against India's 100, suffered a jolt as soon as the match started with their key midfielder Anton Zemilanukhin being stretchered out after a collision with Gurpreet in the fourth minute. Edgar Bernhardt took his place.
The 15th minute was all about Kyrgyz onslaught which kept the sizable crowd at the Sree Kanteerava Stadium quiet.
During this period, the visitors had most of the ball possession with the Indians leaving a lot of space in the midfield. It was due to the brilliance of Gurpreet India did not concede a goal in the 15th minute.
Bakhtiar Duyshobekov had a low shot from a nice buildup but Gurpreet brilliantly saved diving to his right.
India slowly clawed their way back into the match and even threatened to take the lead soon.
In the 23rd minute, Jakichand Singh was in the clear at the right top edge of the box after being released by Chhetri but he was in two minds whether to shoot or pass and wasted a fine move.
Three minutes later, Kyrgyz goal was under threat as Jackichand sent a nice long pass to Chhetri whose first touch inside the box with his left foot was out of control but Holycharan Nazary was there but he shot straight to the goalie.
India had another chance in the 31st minute, off a quick throw-in from the left flank by Eugenson Lyngdoh but Jeje's left-footed shot was brilliantly saved by the goalkeeper.
India was lucky not to concede a goal in the 55th minute as Ahlidin Israilov's left-footer hit the upright. India responded immediately on the counter but Chhetri could not put his shot down in front of Kyrgyz goal off a Nazary delivery from the left.
The Kyrgyz were doing all the attacking after the resumption and the Indian defence was in tatters in the 60th minute and Jhingan had to make a last-ditched clearance in front of the goal after Gurpreet was out of line.
But it was India who took the lead in the 69th minute against the run of play. In a quick counter-attack, Chhetri got the better of at least three Kyrgyz players at the middle of the park and then sent the ball for Jeje.
The Mohun Bagan striker lobbed the ball beautifully over a Kyrgyz defender to find his darting skipper, who made no mistake in firing his shot past the goalkeeper to send the crowd into a frenzy.
India could have won the match with a better margin but for the two chances, they wasted in the additional injury time of four minutes.
Chhetri sent Robin Singh, who substituted Jeje in the 80th minute, on the clear in the first minute of the injury time but the striker shot over with the goalkeeper at his mercy.
In the final minute of the added time, Chhetri himself was on the verge of scoring his second of the night but he also shot over in haste.
India's next match is against Macau, an away game, on September 5.