Mali were the highest-ranked team in action on Sunday at 39th in the world, but they were upset by the 124th-ranked Squirrels thanks to Razak Omotoyossi's 18th-minute goal at the Stade de l'Amitie.
Nigeria opened their Group F campaign with a hard-fought win over Namibia.
John Utaka's first-half strike was disallowed and it looked as though the Super Eagles would have nothing to show for their dominance of the game, but Ikechukwu Uche popped up with a deserved winner 10 minutes from time.
The 2010 World Cup hosts South Africa had to come from behind to earn a point against Ethiopia in Group A.
Said Saladin put the underdogs ahead on the half-hour mark, but Katlego Mphela saved Bafana Bafana's blushes with a 77th-minute equaliser.
Angola were also denied maximum points by Uganda, who grabbed a dramatic late equaliser in the Group J clash at the Cidadela.
Emmanuel Okwi was Uganda's hero, snatching a point after the hosts had led for 80 minutes through Djalma Campos' eighth-minute goal.
Ibrahima Traore scored the only goal as Guinea scrapped to victory over Zimbabwe in Harare in Group G.
Group E remains all square across the board after Gabon were held to a goalless draw in Niger, matching Saturday's scoreline between Burkina Faso and Congo.
Togo and Libya drew 1-1 in Group I. Kalen Damessi gave Togo a 14th-minute lead but Ahmed Zouay equalised within a minute.
The other game in the group saw Jordan and Iraq share a 1-1 draw.
A trademark long-range strike from Nashat Akram gave the visitors the lead in the 14th minute but Jordan equalised two minutes before half-time when keeper Mohammed Kassid fumbled Baha Suleiman's long-range shot into the path of Ahmad Ibrahim, who finished from close range.
In Group A, Iran produced a late sucker punch to snatch an ill-deserved 1-0 win in Uzbekistan.
The hosts dominated the game but failed to take their chances and Mohammad Khalatbari rounded off a 94th-minute counter-attack with a calm finish to rub salt in their wounds.
Elsewhere in Group A, Qatar won 1-0 in Lebanon in the day's final match.
Lebanon had only themselves to blame, as Andres Quintana seized on Ramez Dayoub's poor back-pass to put the visitors ahead in the 64th minute and Youssef Mohamad missed a glorious stoppage-time chance to level the match.