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.
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.
Belenenses' rivals for the European places, Vitoria Guimaraes, travel to mid-table Moreirense on Saturday.
