As in their opening defeat to Gabon, the beaten 2013 finalists created plenty of chances but were unable to find the net - leaving their hopes of progressing rom Group A hanging by a thread.
Alain Traore struck the post twice in the first half but joined Jonathan Pitroipa in spurning opportunities to break the deadlock after the interval, when Equatorial Guinea - spurred on by a vocal home crowd - grew in confidence and threatened to snatch victory.
Put rued his player's profligacy after the 2-0 reverse to Gabon and was frustrated to be repeating himself when he spoke to reporters after the match at the Estadio de Bata.
"The match should have been settled in the first half," he said.
"Like against Gabon we had several chances. Our problem at the moment is finishing.
"We lack confidence. Or maybe it's bad luck, I don't know.
"We create many opportunities and that means that we play well. But you must finish those chances, of course."
Burkina Faso will conclude their group campaign against Congo, who drew 1-1 with Equatorial Guinea first time out and faced Gabon later on Wednesday.
Watch every match of the Africa Cup of Nations LIVE on British Eurosport HD or sign up to Eurosport Player and follow the action on mobile, tablet and other devices: www.eurosportplayer.co
