Benfica never recovered after Roberto fired the hosts ahead in the third minute as more doubts surfaced following a tumultuous close season which saw coach Jorge Jesus defect to arch-rivals Sporting.
Roberto drilled the ball past Julio Cesar after quick-thinking Ivo Rodriguez unlocked the Benfica defence by cheekily slipping the ball between two opponents.
Incredibly, the win left Arouca, led by former Angola coach Lito Vidigal, top of the table as the only team with six points from their opening two games.
"We weren't efficient enough, we had enough chances to score two or three goals," said Benfica coach Rui Vitoria.
"We had more than 20 shots but, no matter how much we tried, there was always the foot or the body of an Arouca player in the way."
Sporting were held 1-1 at home by Pacos de Ferreira on Saturday while Porto chalked up the same scoreline at Maritimo.
It was the first time since May 2013 that none of the three big Portuguese sides won on the same matchday.
(Writing by Brian Homewood in Berne; editing by Ken Ferris)
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