Rodrigues' audacious back flick ensured Cape Verde finished with four points in third place in the standings. They are likely to advance as one of four best third placed finishers.
Rodrigues had been a surprise omission from the starting line-up but underlined his ability soon after coming on.
Aboubakar fired home a left footed shot after a botched clearance from the Cape Verdians, adding to a double scored in each of the opening two matches.
But Cameroon were unable to end the group phase with three victories, which had been their ambition.
"It was difficult opponent who made things tough for us," Aboubakar told reporters.
"It was difficult to win although we wanted to finish with a 100% record. But we must not be negative about it because we are through."
Aboubakar also missed a close-in chance in the second half, but overall Cameroon had limited chances in the match at the Olembe Stadium.