After seeing Uganda upset DR Congo earlier in the day, minnows Madagascar came close to producing a shock result of their own as second-half goals from Anicet and Andria turned the match on its head.
But Guinea, who earlier led through Sory Kaba's smart strike, equalised with a Francois Kamana penalty, sparing their blushes in Alexandria.
Liverpool midfielder Naby Keita appeared as a substitute, returning from an adductor injury sustained in Champions League action last month, yet Guinea were forced to settle for a point in Group B.
Kamano shaped a superb early effort just past the right-hand post from 20 yards, then Julian Jeanvier saw his downwards header deflected against the outside of the same upright.
The Guinea opener soon followed as Amadou Diawara lofted a gorgeous pass in behind the Madagascar defence and Kaba skillfully beat goalkeeper Melvin Adrien with a twisting lob before passing into an empty net.
But Madagascar were level four minutes into the second half with their first AFCON goal through Anicet, flicking unmarked past Aly Keita from Andria's left-wing corner.
Guinea almost restored their lead when Kaba dragged a low shot against the post, but instead they sensationally trailed as Andria found time and space beyond the back line to control a looping ball and finish coolly.
Keita was called from the bench, yet it was Ibrahima Traore's pace on the counter that drew a desperate lunge from Romain Metanire, allowing Kamano to roll in the spot-kick to earn a share of the spoils.