A forgettable 90 minutes yielded few chances and no goals, leading to spot-kicks, where Javier Balboa and Raul Fabiani missed Equatorial Guinea's first two efforts to leave Cedric Mongongu with the honour of netting the decisive penalty to make it 4-2.
Crowd violence overshadowed the hosts' semi-final defeat at the hands of Ghana, with 36 people injured as projectiles were aimed at opposition players, officials and fans.
The Confederation of African Football (CAF) hit the Equatorial Guinean Federation with a $100,000 fine and ruled that it must pay medical costs for the injured parties.
It had been suggested that Saturday's match may have to be played behind closed doors, but ultimately it took place at a sparsely populated Nuevo Estadio de Malabo - and there was little to shout about in a drab first half.
Equatorial Guinea shaded the first 45 minutes, with Robert Kidiaba marginally the busier goalkeeper, though Yannick Bolasie spurned the half's best chance when he blazed over from a good position.
DR Congo, beaten 3-1 by Ivory Coast on Wednesday to miss out on their first final since 1974, saw two excellent chances come and go early in the second half - Felipe Ovono saving superbly from Chancel Mbemba, and substitute Dieumerci Mbokani tamely side-footing straight at the goalkeeper soon after.
Ultimately penalties were required to separate the teams, and Equatorial Guinea could not recover from missing the opening two attempts as they had to settle for fourth.
Esteban Becker's side had made an enterprising start and threatened first as Balboa's cross caused problems for Kidiaba, with Mongongu having to step in to tidy up.
Kidiaba was busy again in the ninth minute as a penalty-box scramble ended with the goalkeeper denying Emilio Nsue from close range, while Cedric Makiadi's woeful free-kick delivery at the other end underscored a shoddy opening 20 minutes for DR Congo.
And yet they could have taken the lead just before half-time, only for Bolasie to fire well over the bar after racing through on goal.
Ovono produced a stunning one-handed save two minutes after the interval to keep out Mbemba's header from a corner.
But it was wasteful finishing that frustrated Florent Ibenge's men six minutes later, when Mbokani - on at half-time - meekly shot goalwards following Cedrick Mabwati's superb run and cutback.
Equatorial Guinea went close at the other end, but Nsue failed to find a way post Kidiaba when through one-on-one.
The game continued to open up as both sides looked keen to avoid a shootout, but, after Nsue shot wide deep into stoppage time, penalties were needed to settle matters.
Balboa blasted the first one high and wide, with Kidiaba saving Fabiani's effort, while Mongongu demonstrated a much cooler head to leave DR Congo celebrating and the hosts in tears.
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