Lyngdoh, playing for the first time for Pune this season after turning out for Bengaluru FC in AFC Cup final, struck the match-winner in the 89th minute at Mumbai Football Arena in a game which saw both the teams stonewalling each other's attacks for the most part.
Mumbai goal-keeper Albino Gomes came out of his line to collect a Narayan Das cross from the left but he fumbled and the ball fell on Lyngdoh who had all the time in the world to bulge the net.
Mumbai were the stronger team off the blocks as they tried to feed their strikers with long balls but the visitors were equal to the task and averted any danger.
The home side soon suffered a blow as Leo Costa had to limp off with a groin injury and Thiago Cunha was brought on. The change almost paid dividends with Cunha setting up Sehnaj Singh off an Edel Bete fumble but the youngster put his shot over the bar.
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At the other end, Mohamed Sissoko combined with Rahul Bheke brilliantly quite a few times but they failed to break down the Mumbai backline.
The game slowed down as Sunil Chhetri, who is also playing for the first time for Mumbai this season after doing Bengaluru FC duty, and Diego Forlan indulged in some sublime one-touch football but a goal still eluded them as both teams headed into the tunnel at half-time goalless.
Mumbai once again went on the attack as Forlan found Krisztian Vadocz on the far post but the Hungarian was unable to find the target. It just did not seem like Mumbai's night when Forlan's free-kick was pushed onto the crossbar by Bete.
Pune brought on Jesus Tato soon and his introduction invigorated the visitors. He put in quite a few good balls and one of the rebounds was drilled in by Jonatan Lucca but it went straight to Albino Gomes.