Thakur's double strike helped Punjab to a 3-1 advantage, after the teams were level 1-1, before Devinder Walmiki's penalty corner strike two minutes from the time narrowed the margin of defea.
The first two goals of the well-fought contest were notched by medio Tariq Aziz in the second minute for Punjab which was neutralised by Joga Singh's effort in the 12th minute of the match.
The victory took Punjab's points tally to 13 from seven games, the same as Bhopal Badshahs who were pushed to the second spot because of Punjab's superior goal difference.
The loss, their third in seven games, spoilt Marines hopes of rising from the fourth spot as they remained on 10 points.
In a well-contested clash, the visitors took a second minute lead when Pakistani Tariq Aziz pushed in from close range before the Marines drew level 10 minutes later through their leading scorer Joga Singh, his sixth goal.
The visiting team kept up the pressure on Mumbai with some fast-paced forays after taking the second minute lead and could have scored again following a defence-splitting through ball from Aziz to Mandeep Antil, who shot on the run just wide of the far post.
Punjab forced their first penalty corner and Adrian brought off a good save to foil the visitors.
Just when it seemed the Marines will have to stay 0-1 behind in the first quarter came the opportunistic strike by their sharp-shooter Joga.
Left free inside the 'D', the tall Joga put his stick to deflect in a long through pass from midfield essayed by Xess Banmali to help the hosts draw level in the 12th minute.
The two teams ended the first quarter level at 1-1. No goals were scored in the second and third quarters with both the teams mounting raids constantly without success.
Punjab took the lead again in the last quarter, in the 56th minute, following their third penalty corner taken indirectly when Thakur pushed the ball and stood waiting for the shot taken by Harpal Singh to deflect the ball in past Adrian's right.
Thakur was on hand unmarked on the right side of the goal six minutes later when a defensive error saw the ball come to him and he made no mistake.
Right through the match full back Ajmer Singh was a tower of strength for the Marines in front of his skipper while the visitors were well-served in defence by their custodian Dinesh Ekka, who foiled the home team's forays on quite a few occasions.
The moves were initiated tirelessly by respective midfielders V S Vinaya for Punjab and Devinder Walmiki, Hari Prasad and Troy Sutherland for the home team, but the Marines also were guilty of missing a few gilt-edged chances.
Star Punjab forwards and Olympians - Prabhjot Singh and Thakur ? were bottled up well after shining initially, till they started coming into their own in the final quarter to effectively seal the match in their side's favour.
Aziz started the match in impressive fashion but faded away after his initial flourish. The visiting team also lacked an effective penalty corner specialist. They got three in all and scored off one, in an indirect manner.
Chandigarh Comets edge Delhi Wizards 1-0
Chandigarh Comets beat Delhi Wizards 1-0 as Gurjinder Singh scored the winner in the 63rd minute through a penalty corner in Delhi.
Today's Matches (March 15)
7.00 pm Pune Strykers vs Chennai Cheetahs (Pune)
9.00 pm Delhi Wizards vs Bhopal Badshahs (Delhi)