Acre struggled to defend the jab for most of the fight and was bleeding from his nose after the third round. But he took control in the sixth and floored Rojas with a left hook to the stomach 37 seconds into the round.
Rojas (26-11, 18 KOs) got up from the canvas, but Arce wasted no time in delivering a series of body shots that forced referee Joe Cortes to call the fight at the 2:01 mark.
It was Arce's first fight since April when he lost the WBC flyweight title to Cristian Mijares to break a string of 26 consecutive victories. Now, the 28-year-old wants another shot at Mijares, who gave him his first loss since 1999.
Arce (47-4-1, 36 KOs) had defended his flyweight title four times before losing to Mijares.
The rivalry increased this week when Mijares said Acre should concentrate on fighting Rojas, who at 5 feet, 11 inches is 6 inches taller instead of worrying about a possible rematch.
Mijares even predicted Rojas would win because of his height and reach advantage.
Arce was clearly uncomfortable against the taller Rojas, but proved to be more experienced in the decisive round. Arce improved to 17-2 with 13 knockouts in champion fights.
WBC light flyweight champion Edgar Sosa (29-5, 15 KOs) stopped Lorenzo Trejo (27-16, 15 KOs) in the ninth round.
Lightweight Jorge Paez Jr. (17-1, 10 KOs) continued to win by scoring a six-round decision over Alain Hernandez (9-6-1, 6 KOs). The scores were 59-55, 58-56 and 60-54.