Salah added to an opener from Trezeguet in Cairo as Egypt toiled for almost 70 minutes before they broke down the Mauritania defence to move six points clear at the top of Group C at the midway point of the qualifiers.
Tunisia were heavy favourites after starting their campaign with two wins, but despite 15 goal attempts fell to a lone strike from Rafiki Said just past the hour mark.
It was Tunisia's first home defeat in Cup of Nations qualifiers since 2010 but they remain on top of Group A with six points from three games. Comoros are behind them on five points.
The top two teams in each pool advance to the 24-team finals in Morocco next year.
Nigeria needed a late goal to seal a 1-0 home win over Libya as German-born midfielder Fisayo Dele-Bashiru netted four minutes from the end to spare the blushes of the 2023 finalists.
It was an important win for Nigeria who top Group D and are five points ahead of third-placed Rwanda with three games remaining.
Ivory Coast brushed aside Sierra Leone 4-1 in San Pedro as Franck Kessie scored a brace, both netting and missing a penalty. Nicolas Pepe was also on target as they made it three wins from three.
Sadio Mane and Nicolas Jackson were both on the scoresheet for Senegal as they beat 10-man Malawi 4-0 in Diamniadio. Senegal and Burkina Faso are each on seven points at the top of the pool and favourites to qualify.
Cameroon eased to a 4-1 victory over Kenya as Bryan Mbeumo took his Premier League form with Brentford onto the international stage with a goal, to go with a penalty from Vincent Aboubakar, a first international strike for Martin Hongla and a goal from Christian Bassogog.
South Africa recorded the joint second-biggest win in their history as they thumped Congo 5-0 in Gqeberha to continue their good form under coach Hugo Broos. Victory over the same opponents in Brazzaville on Tuesday will see them qualify.
Teboho Mokoena netted a brace to go with goals from Bathusi Aubaas, Lyle Foster and Iqraam Rayners.
Bevis Mugabi scored the only goal as group leaders Uganda beat South Sudan 1-0 in the other fixture in the pool.
There were also wins for Equatorial Guinea, Benin, Angola and Mali, but Avram Grant's Zambia were held to a surprise 0-0 draw at home by Chad that leaves them in second place with four points from a possible nine in their pool.
