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The home side began the match on the front foot as Jonas Martin was teed up inside the box, but he put his effort wide of the post.
In the second half, Montpellier capitalised on their numerical advantage to equalise as Boudebouz raided down the flank and lifted a cross into the box for Camara to head into the net.
The home side took the lead in the 63rd minute through Ninga as Camara turned provider by firing a low ball across the face of goal for the midfielder to convert from close range.
Guingamp tried to rally late in the game and came close to finding a leveller through Yannis Salibur, but he put his strike past the post.
The visitors pressed forward in stoppage time, but Marcus Coco was unable to hit the target with his effort from inside the area, which resulted in his team falling to a narrow defeat.
Montpellier rise to 13th in the table, while Guingamp drop to 18th.