Second-half goals from Yuta Kinowaki (47') and Henry Kisekka (60') were enough to seal the three points for the home side.
Despite Eze Kingsley coming back into the Bagan lineup, captaincy duties were stripped off of him and handed over to Aser Dipanda for his red card in the Kolkata derby. Shankar Lal Chakraborty stuck with his new-found formation as Henry Kisseka started from the left wing.
A 6-1 hiding at the hands of Real Kashmir prompted three changes in the Shillong Lajong XI. Goalkeeper Neithovilie Chalieu and striker Sheen Stevenson were relegated to the bench as Novin Gurung was not involved in the matchday squad. Kitboklang Pale got his first career start.
Goalkeeper Phurba Tempa Lachenpa justified his selection with two saves of the highest order inside the first twenty minutes. First, Dipanda chested the ball down inside the box and tested the Sikkim-born but he came off with a right-footed block.
Moments later, Omar Elhusseiny failed to penetrate the Lajong net after some good build-up play from Dipanda and Kisseka in quick succession as Lachenpa pulled off a diving save.
Bagan broke the deadlock within two minutes of resumption after the lemon-break courtesy of a Yuta Kinowaki screamer from the edge of the box. Aibanbha Dohling's headed clearance fell for Kinowaki who wrapped his laces around the ball to score a spectacular goal against his former side.
After falling back, Lajong started to show some urgency in midfield. Samuel Lalmuanpuia dribbled past two Bagan shirts before setting up Samuel Kynshi in front of goal. Sankar Roy was out of his line but the shot-stopper pulled off a brilliant save from close range to keep the score unchanged.
At the hour mark, Bagan doubled their lead through Kisekka following a defensive howler by Kynsailang Khongsit. Dohling's feeble clearance fell for DIpanda who fired a shot at goal. It was a moment of brain-fade from Khongsit who failed to clear his lines and Kisekka just pushed the ball into an empty net from inches of the goal-line.
Bagan could have added to their tally but it was Lachenpa who continued his brilliance to prevent an embarrassing scoreline for Lajong.
Bagan climbed to the fifth spot with 15 points from nine matches whereas Lajong failed to move clear of the relegation zone.
At the back of this win, the Mariners will hit the road to take on NEROCA on December 28 whereas Lajong will travel down south to face league leaders Chennai City FC a day later.