A brace (36' and 45') from Samuel Kynshi had put the hosts ahead before Willis Plaza and (53') and Anthony Wolfe (71') levelled matters for the visitors. However, a late goal by Mahesh Singh (83') broke Churchill hearts as Shillong swept home all three points.
Rakesh Pradhan was seen making his comeback from injury for the Meghalayan outfit with Kynsailang Khongsit giving way while Mahesh Singh replaced Lalawmpuia Hnamte in the starting XI.
On the other hand, the Goans were lined up with just three foreigners. Khalid Aucho and Nallappan Mohanraj did not make the trip to Shillong while Anthony Wolfe started on the bench. Cavin Lobo was handed his first start of the season with Jovel Martins and Nicholas Fernandes also brought in for the tie.
The attacking trident of Kitboklang Buam, Phrangki Buam and Mahesh Singh were causing all sorts of problems to the Churchill backline in the opening exchanges and forced goalkeeper James Kithan to save an attempt from Pradhan from a corner in the 11th minute.
Moments ealier too, Mahesh was in a very good position after being found in the box by Pale but an untimely slip caused him to lose the ball to Hussein Eldor.
The visitors managed to create their first opening in the 18th minute but Nichoas' cross from the left was disappointing and was intercepted by Phurba Lachenpa before it could make its way to Plaza.
Lajong continued to attack and Churchill coach Petr Gigiu was forced into making his first change as he sacrificed Chesterpoul Lyngsoh to bring in Anthony Wolfe.
However, it was the home side celebrating the opener in the 36th minute when Mahesh made a quick turn towards goal and sets up Kynshi who slotted the ball past Kithan from inside the box.
Just before half-time, Alison Kharsyntiew's side had a two-goal lead going into the break as Kynshi converted from the spot after Rowilson Rodrigues was found guilty for a push in the back of Buam.
Kithan still kept the scoreline humble to a certain extent as he pulled off another save from a one-on-one situation with Pale.
Minutes into the second session of play, Plaza stepped up to tap in a Nicholas Fernandes cross from the left to make it 2-1 in the 53rd minute.
Soon after, Lajong could have regained their two-goal lead off a through ball by Samuel Lalmuanpuia as Mahesh helped the ball past Kithan towards the left side, but the latter's attempt from an acute angle didn't have enough curl on it.
Then, out of the blue, Wolfe outjumped Kenstar Kharshong to nod in Eldor's long lob to make it 2-2 in the 70th minute.
However, Mahesh took a pass from Lalmuanpuia and struck from the edge of the box put Lajong back in front in the 83rd minute.