Kaba Diawara's side started their final Group B match with one foot seemingly in the knockout stage, but Zimbabwe pulled off an upset to end its 14-match winless run in Yaounde on Wednesday (AEDT).
Captain Knowledge Musona rose unmarked to open the scoring for Zimbabwe - with no chance of qualifying after losing their two other games - after 26 minutes, heading home Never Tigere's cross from six yards out.
Kudakwashe Mahachi doubled Zimbabwe's lead two minutes before half-time, with goalkeeper Aly Keita badly at fault as he failed to keep out the midfielder's shot from outside the penalty area.
Guinea looked a totally different side after the break and Naby Keita halved the deficit four minutes into the second half, bursting forward and unleashing a rasping left-foot strike from outside the box that flew into the far corner of the net.
Zimbabwe came under increasing pressure but held on for their first AFCON win since 2006, while Syli Nationale.will have to wait to learn if they will qualify as one of the best third-placed finishers after Senegal and Malawi drew 0-0 to finish top and second respectively.