An early goal from Zohmingliana Ralte denied the hosts' hope of a sure berth in next season's top bracket in the country.
With 20 points from 19 matches, they were just two points ahead of bottom-placed Bharat FC.
Ralte headed the solitary goal of the match for visiting Pune FC as early as in the fifth minute when Lajong's defender failed to clear an Arata's corner.
Lajong manager Thangboi Singto made four changes to his team's line up when Uilliams, David Gaite, Jibon Singh and M Singh were out.
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Ten minutes later, Glen was brought down by Sobrosa just outside the box but a Penn Orji's shot hit the wall.
Several other chances followed but luck was not on their side even as another powerful right footer from Len Doungel went just above the bar 20 minutes after the lemon break. Another chance came when Glen found the net near the one and a half hour mark but was ruled offside.
Pune FC went on to control the match and restrict the ball to the midfields in the second half of the match.
The home favourites will lock horns with East Bengal this Saturday at home.