An early strike kept the visitors fine away record of three wins in four games intact.
The only goal of the game came after only nine minutes. Brian Fairbairn sent over a free-kick from the left wing to the back post where the ball was knocked down into the path of Paul McManus, who scored his ninth goal of the season from close range.
Raith were impressive from the early stages, but after going behind it was Peterhead who dominated for long spells.
The home side's best chance came in the 36th minute when Jamie Buchan sent a shot on to the junction of the post and cross- bar.
Rovers' Scotland under-21 goal-keeper Alistair Brown kept his side in the game with several saves. The best came soon after the goal. Scott Michie raced clear but Brown denied him, saving his shot with his left leg.
Peterhead continued to dominate in the second half, but Raith looked like having the cutting edge to get them back into the game. Their luck was summed up by a shot from Graeme Sharp 10 minutes from the end when his effort from six yards ended up heading towards the corner flag.