The Bees, who were only denied a tilt at Championship football this season after being beaten in the play-off semi-finals by Swansea in May, captured their second 1-0 success to leave manager Leroy Rosenior a happy man.
But they could count themselves lucky as debut striker Chris Moore, signed in the summer from Dagenham and Redbridge, made the most of an almighty blunder by Harper with 19 minutes left.
Harper had been outstanding in Northampton's 2-2 draw at Crewe on Saturday when he tried to shield a ball into touch late on; Moore robbed the goalkeeper before creating himself an angle and slotting the ball into an empty net.
It was rough on John Gorman's men, who were anxious to continue their exciting start after promotion last season, but ultimately they slipped to a first league defeat since March after ending last season on a high.
The Cobblers had the best of the chances in the first half with Andy Holt seeing a 25-yard drive flash inches wide in the 31st minute, while a cross from the same player brought a close-range header by Pedj Bojic which was blocked by goalkeeper Stuart Nelson - one of four changes for the Bees after their opening day success against Blackpool.
Nelson also earned his corn before the break when he reacted smartly to parry away a drive by Sam Aiston whose pace was a cause of trouble to Brentford all night.
The second half began with Joe Burnell firing over for the home side but Brentford finally began to create some chances, with Thomas Pinault advancing before letting fly with a shot which shaved Harper's left-hand post.
Moore missed the best chance of the match in the 66th minute when he left defender Luke Chambers on the ground but with the goal seemingly at his mercy he screwed his shot wide.
Moore was shortly to make amends thanks to Harper's miserable moment but this only prompted a fierce late rally from the home side as they fought for an equaliser.
Nelson made a finger-tip save to deny Andy Kirk and the goalkeeper also fumbled a Scott McGleish shot before doing well to hang onto a raking low drive by Bradley Johnson.