Jorge Simao's men consolidated their hold on sixth position with a second straight victory, moving one point behind fifth-placed Vitoria Guimaraes - who occupy the final UEFA Europa League spot.
Pele's 53rd-minute penalty was enough for the visitors to Arouca's Estadio Municipal.
The Portuguese midfielder's spot-kick was placed perfectly in the bottom-left corner of the net, denying Arouca goalkeeper Mauro Goicoechea, who guessed correctly but was still beaten.
Belenenses' penalty was awarded for a handball from Arouca's Diego, the Brazilian defender punished for leaving an arm flailing when attempting a header.
Captain Carlos Martins hit the post for Belenenses in the first half, while Joris Kayembe spurned a gilt-edged chance after 49 minutes.
Yet Pele then broke the deadlock and Arouca could not find a reply, their best chance coming when a curling free-kick from Iuri Medeiros forced Hugo Ventura into a diving save.
The loss leaves Arouca (23 points) just four points above the drop zone, with Gil Vicente (19) and Penafiel (18) still to play at the weekend.
Belenenses' rivals for the European places, Vitoria Guimaraes, travel to mid-table Moreirense on Saturday.
