Prolific Liverpool scorer Salah tested positive for Covid-19 after arriving in Cairo for international duty and a subsequent test produced a similar result.
Apart from missing back-to-back matches against Togo, he could also be ruled out of the next two matches for his club, against leaders Leicester City in the Premier League and Atalanta in the Champions League.
Salah has shown no symptoms of coronavirus and Egyptian Football Association medical staff have been in contact with counterparts at Liverpool.
The two-time African Footballer of the Year award winner has had an unlucky Cup of Nations campaign having suffered an injury against Kenya last November, which ruled him out of a match in the Comoros.
El Wensh -- also known as Mahmoud Hamdy and Mahmoud Attia -- beat goalkeeper Malcolm Barcola on 54 minutes with a header from point-blank range after Togo failed to clear a softly-awarded free-kick.
It sufficed to give record seven-time African champions Egypt a first win in Group G after draws with Kenya and the Comoros.
The Pharaohs will face Togo again in Lome Tuesday before visiting Kenya and hosting the Comoros next March, and the group winners and runners-up qualify for the 24-nation tournament in Cameroon.
Comoros and Egypt have five points each, Kenya three and Togo one after three rounds in a section where all the contenders will believe they still have a chance of making the finals.
Togo, who are guided by legendary French coach Claude le Roy, can draw encouragement from having most of the possession after falling behind in Cairo.
Meanwhile, Benin closed the gap behind Group L leaders Nigeria to one point after defeating Lesotho 1-0 in Porto-Novo through a first half goal from Jodel Dossou.
The match-winner was a French affair with Dossou from second-tier Clermont the scorer and Khaled Adenon from third-tier Avranches the creator.
In Group D, the Democratic Republic of Congo and Angola remained third and fourth behind Gabon and the Gambia after a drab 0-0 draw in Kinshasa.
Two-time African champions DR Congo had to make many changes to the original squad because of positive Covid-19 tests, injuries and travel difficulties.
The three Saturday qualifiers completed matchday 3 and matchday 4 starts Sunday and continues through Tuesday.
Mohamed Salah EGYPT