Gabon fell to a 1-0 defeat to Mozambique in Maputo as they suffered without injured star striker Pierre-Emerick Aubameyang.
Aubameyang, 26, has already scored 22 goals in all competitions for Borussia Dortmund since the start of 2015-16, but was ruled out with a muscular injury prior to kick-off in a major blow for Jorge Costa's side.
Mozambique took advantage by keeping a clean sheet, with Helder Pelembe scoring the only goal of the game on 54 minutes.
The two teams meet again in Gabon on Saturday, with the winners over two legs progressing to the final CAF group stage for the 2018 World Cup in Russia as 40 African teams are cut down to 20.
In Wednesday's other first-leg game, Zambia battled to a 1-0 away win over Sudan in Karima.
Winston Kalengo's goal in the 28th minute proved decisive to make the 2012 African Cup of Nations winners strong favourites to progress.
The second leg of that tie takes place on Sunday in Ndola.