The result was enough to seal the title on the away-goals rule, following a 2-2 draw in Kinshasa last weekend.
It is the first time Setif have won the tournament since 1988, handing Kheireddine Madoui's side a lucrative $1.5million in prize money and a place in the FIFA World Club World Cup in Morocco this December.
It also completes a remarkable success story for a team who nearly did not enter the competition due to the Algerian Football Federation expressing concerns that the country's teams would not be able to compete with the rest of Africa.
Setif did much of the early pace-setting during a cagey opening 45 minutes of the second leg, although Vita Club, from DR Congo, went close through Guy Lusadisu Basisila five minutes before half-time.
The majority of a sell-out 35,000-capacity crowd in Blida was sent wild with delight after 50 minutes, when El-Hedi Belameiri's cross eluded a packed penalty area to find Sofiane Younes at the far post, and he poked a shot home from close range.
That joy was cut short five minutes later however, when Lema Mabidi added to his brace in the previous leg by smashing home an unstoppable effort, after Setif had failed to clear their lines.
But despite a nervy finish, Setif held firm to become only the second team from Algeria to claim two CAF Champions League titles.
