Embiid appeared to roll his left ankle when he tripped over teammate Georges Niang with 5:53 remaining in the fourth quarter. He writhed in pain on the ground and was attended to by a trainer before hobbling to the bench at Wells Fargo Center.
The Sixers center played the game out but limped throughout yet nailed a three-pointer to make it 105-102, before Timberwolves top scorer Anthony Edwards steadied it with his second triple of the game.
Embiid finished with 32 points, including making 18-of-20 from the free-throw line, with nine rebounds, six assists and three steals for the Sixers, who were without James Harden and Tyrese Maxey due to foot injuries.
Shake Milton added 27 points, while De'Anthony Melton made five three-pointers in his 19-point haul. Melton's three with 29.1 seconds remaining moved the 76ers within one point, before he missed a lay-up and Edwards iced the game from the stripe. The Sixers had trailed by 20 points but rallied with a 25-15 fourth quarter.
For the winners, Edwards had 25 points with five rebounds and five assists, while point guard D'Angelo Russell scored 19 points with seven assists.
The result leaves both sides with 8-8 records, with the Timberwolves having won three straight. Embiid's 32 points means he is averaging 41.25 across his past four games.
Trae shines as Hawks win with OT buzzer-beater
Young took an inbound pass with 3.8 seconds remaining in overtime with scores tied, racing clear as Griffin - who is the son of Raptors assistant coach Adrian Griffin - got behind the defense, allowing the Hawks guard to find him wide open for a routine lay-up in the nick of time.
Atlanta hauled in a seven-point deficit with 2:36 to go in the fourth quarter, led by Young, who finished with 33 points on 12-of-21 shooting with 12 assists. Scottie Barnes had a season-high 28 points for injury-hit Toronto, who only dressed nine players.
George hurt as Clippers blow out Spurs
Paul George hit three first-half three-pointers before being ruled out with knee soreness at half-time while Kawhi Leonard's impact was limited again but the Los Angeles Clippers blew out the San Antonio Spurs 119-97.
George played 15 first-half minutes, scoring 21 minutes on five-of-eight three-point shooting, while Leonard played 22 minutes for 11 points with four assists in his second game back after stiffness in his surgically repaired knee.
Norman Powell came off the bench to score a game-high 26 points, with five-of-seven three-point shooting, as the Clippers improved to 9-7. The Clippers hit 13 first-half triples and finished with 21 for the game on 53.8 per cent three-point shooting.