His fellow Argentine Maxi Moralez completed the scoring after another slip-up by third-placed Napoli, who continued their habit of dropping points against mid-table opposition.
Second-placed AS Roma's match at home to Parma was called off after only eight minutes when incessant heavy rain left the pitch waterlogged, giving Juventus a chance to extend their six-point lead at the top at home to Inter Milan in the evening (1945 GMT).
Lazio won 2-0 at Chievo in their first match without Brazilian midfielder Hernanes, who joined Inter in the transfer window, and bottom club Catania came from behind three times to hold Livorno 3-3 after a six-goal second half.
Swiss midfielder Innocent Emeghara scored twice and Paulinho converted a penalty for Livorno while Argentine trio Gonzalo Bergessio, Pablo Barrientos and Sergio Almiron replied for the Sicilians in a match featuring two teams in the bottom three.
Sassuolo, also in the drop zone, gave new coach Alberto Malesani a losing start going down 2-1 at home to Hellas Verona.
Benitez surprisingly started with forwards Gonzalo Higuain and Marek Hamsik on the bench but it backfired in a dismal first half in Bergamo, where home fans entertained themselves by repeatedly letting off smoke bombs behind the goal.
Atalanta went ahead two minutes after halftime when Blerim Dzemail gave the ball away and Denis scored with a low, powerful shot which was badly misjudged by Pepe Reina.
Higuain came on for Napoli and quickly forced Andrea Consigli to make his first save of the game just after the hour, only to see Atalanta score again almost immediately.
This time, Napoli midfielder Gokhan Inler, on the end of the area penalty area, made a complete hash of a clearance which went straight to Denis who fired past Reina.
Moralez added the third in the 70th minute after Federico Fernandez slipped, allowing him to slot the ball past Reina.)