The result of the Group G dead rubber maintained the 100 per cent record of the 'Pharaohs' as they chase a first FIFA World Cup appearance since the 1990 finals in Italy. Aboutrika is the ninth Egyptian footballer to reach the 100-cap milestone, while retired compatriot Ahmed Hassan holds the world record with 184 national team appearances.
A draw in Cairo on September 16 will decide who Egypt face in a two-leg play-off during October and November with the winners securing a place at the 2014 FIFA World Cup Brazil.
Egypt made a disastrous start to the win over Guinea, falling behind after only four minutes when Adam El Abd scored an own goal. A mix-up between El Abd and goalkeeper Sherif Ekrami led to the early bonus for Guinea as they sought to avenge a 3-2 home loss last year.
The home side gradually took control and almost levelled midway through the half when goalkeeper Naby Yattara clawed away a Shikabala free-kick. Ibrahima Bangoura had a half-chance at the other end five minutes later, but his tame effort trickled into the hands of Ekrami.
Early second-half drama saw Guinea captain Kamil Zayatte red carded for handling a goal-bound shot and Aboutrika converted the resulting penalty. But ten-man Guinea hit back six minutes later when Seydouba Soumah beat El Abd to the ball and raced clear to net.
Yattara saved superbly from Shikabala and Guinea substitute Mohamed Yattara was spared embarrassment by being ruled offside after missing a sitter.
Egypt nudged in front again with seven minute left and Aboutrika was involved once more, back-flicking the ball to Mohamed Salah, who rounded the goalkeeper and scored. There was no stopping Aboutrika as he put Amr Zaki through and a drive from the substitute found the net via Mohamed Sakho.
Croatia-based striker El Arabi Soudani was the match-winner in Blida, south-west of Algiers, with a goal for the Desert Foxes six minutes after half-time.
Burkina Faso, Cameroon, Cape Verde Islands, Ethiopia, Ghana, Côte d'Ivoire, Nigeria and Senegal topped the other groups and secured places in the play-offs draw.