The hosts’ semi-final against Ghana on Thursday was halted after missiles were thrown at players and supporters.
Only a small crowd turned out at Malabo stadium, the scene of Thursday’s violence, to see the sides draw 0-0 in normal time.
Defender Cedric Mongongu struck the winning penalty for DR Congo.
Equatorial Guinea were fined £65,000 for the violence following the semi-final, which saw 36 fans injured.
DR Congo defender Gabriel Zakuani had called for his country to pull out of the play-off match following the trouble.
Nick Cavell, commentating for BBC World Service at the play-off on Saturday, said there was an increased police presence around the stadium before kick-off.
Read more at: BBC Sport