The victory marks a strong run of form for the Gunners' U23s, having strolled to a 4-1 win against Chelsea last week with Danny Welbeck getting on the scoresheet against the Blues.
Sanogo had seen an earlier bicycle kick attempt well saved by Pau Lopez, but the goalkeeper was partially at fault as the striker eventually found the net for the Gunners.
Tottenham failed to clear their lines as Carl Jenkinson intercepted a poor attempted clearance from Joe Pritchard, with Sanogo racing onto the rebound and seeing his low effort deflect off Lopez's hands and face into the side of the net.
Both sides had chances in the second half at London Colney, but Arsenal grabbed a second goal to seal the game two minutes from time as Donyell Malen teed up Reiss Nelson to slam home.
Jenkinson was joined in the Arsenal starting XI by fellow right-back Mathieu Debuchy, with both defenders pressing for a recall to Arsene Wenger's first-team squad after Gabriel made himself back-up to Hector Bellerin in their absence this winter.
Sanogo has his work cut out to break into Wenger's first-team plans, with the likes of Welbeck, Lucas Perez and Olivier Giroud all struggling for game time this season as Alexis Sanchez stars in an advanced role with 17 league strikes.