The midfielder produced one of his trademark runs starting in his own half before firing a stunning strike past the despairing keeper, who got a hand to it but was powerless to prevent the ball hitting the back of the net.
Ten-man Ivory Coast fought back from 3-1 down to level the scores, but a late Jeremy Bokila goal condemned them to a second loss of the group stage.
This was the second time in a week the two sides have come face to face in the 2015 Africa Cup of Nations Qualifiers. The Elephants triumphed 2-1 over their opponents last Saturday, with Toure setting up the winner for Max Gradel late on.
At the start of this match, the Ivorians sat three points ahead of DR Congo, but four points behind leaders Cameroon – having played one game less.
Congo took the lead after 21 minutes through Neeskens Keban, but it took Toure just four minutes to level the scores with one of his vintage strikes, having already gone close with a free kick that only narrowly missed the target.
However, things began to look bleak for Herve Renard’s men when their opponents scored twice in 60 seconds to gain a two goal advantage, and the situation got even worse when Franck Kessie was sent off shortly after the half time break.
The Elephants, who started the match as favourites, fought back to 3-3 despite their one man disadvantage courtesy of two goals from substitute and former Chelsea man Salomon Kalou.
Toure carved out another glorious opportunity but was thwarted by the Congo keeper, who just managed to get a hand to his shot which was heading for the inside of the far post.
Bokila fired home the late sucker punch with just seconds of normal time remaining, leaving Ivory Coast third in Group D on goal difference.
Toure’s side conclude the qualifying campaign in November with games against Sierra Leone and Cameroon for the right to progress to January’s finals.