Milan, who were eliminated from the Coppa Italia semi-finals by Lazio on Wednesday, lacked a clinical edge with Krzysztof Piatek only entering the game in the second half and have now won just one of their past eight matches in all competitions.
Italy international Belotti fired home from the spot in the 58th minute following Franck Kessie's foul on Armando Izzo and, after Piatek was thrown on in response, Berenguer sent a fine effort past Gianluigi Donnarumma.
Alessio Romagnoli was shown a straight red card for sarcastically applauding referee Marco Guida with nine minutes remaining as Milan's hopes of qualifying for next season's Champions League were dealt a huge blow.
Andrea Conti, Suso and Lucas Paqueta were booked in a scrappy first half of limited goalscoring opportunities.
Walter Mazzarri was removed from the dugouts for dissent shortly after the restart and Torino were unhappy about not getting a penalty when Belotti went down under pressure Mateo Musacchio.
However, the referee did point to the spot when Kessie felled Izzo and Belotti drilled the spot-kick straight down the middle.
Gattuso sent Fabio Borini and Piatek on and Tiemoue Bakayoko rattled the crossbar with a header from just inside the box as Milan finally displayed some urgency.
Berenguer stopped them from gaining further momentum in the 69th minute when he beat Donnarumma with a looping cross-goal shot from the left side of the box.
Bakayoko went close again with a header that Salvatore Sirigu blocked, but Milan's hopes of salvaging a result ended with Romagnoli's dismissal for dissent.
What does it mean? Champions League race wide open
Victory for Torino – their first against Milan in the league since 2001 – means just three points separates fourth-placed Roma from Lazio in eighth, though Atalanta can increase that to four by beating relegation-threatened Udinese in their game in hand on Monday.
The only boost for Milan is that they have a superior head-to-head record against everyone except Torino in the battle for fourth.
Relentless Belotti reaps rewards
Although the first half saw minimal goal-mouth action, Belotti got five shots away as he kept the Milan defence on their toes. His pace regularly put the visitors on the back foot and he dispatched his penalty with aplomb.
Piatek omission baffling
He may have not scored in his past three appearances, but Gattuso's decision to bench Piatek for the first time since his debut in January backfired. Patrick Cutrone led the line in his stead and although he provided three key passes, the striker failed to register a single shot at goal.
Key Opta Facts
- Milan have won five points in the past seven games - only Parma and Fiorentina (four) have done worse in the same period.
- Torino striker Belotti has scored four goals in his past four home league games.
- Milan and Torino have not conceded a goal in the first half in their past five Serie A outings.