Tunisia and Morocco won for the second time during the FIFA international window, but Senegal drew again and Nigeria lost after winning last weekend.
Reigning African Footballer of the Year Salah has scored 36 goals in 41 appearance for Liverpool this season — 11 less than the record held by Ian Rush.
But Egypt coach Hector Cuper deemed the striker surplus to requirements in Swiss city Zurich and his decision backfired as the Pharaohs were outplayed.
The lone goal came after 29 minutes when Nikos Karelis soared unmarked to nod a cross into the net.
Greece dominated the second half against the seven-time African champions, who are back at the World Cup after a 28-year absence.
Salah scored last Friday against Portugal before Egypt conceded two stoppage-time goals to Cristiano Ronaldo and lost 2-1 against the European champions.
Tunisia, returning to the global showpiece after missing the last two tournaments, edged fellow qualifiers Costa Rica 1-0 in French city Nice.
Wahbi Khazri, on loan to Ligue 1 outfit Rennes from English second-tier strugglers Sunderland, scored the winner nine minutes before half-time.
It was the second solitary goal victory within five days for the Carthage Eagles after an own-goal brought success over Iran, another Russia-bound nation.
Ayoub el Kaabi, the nine-goal star of the recent African Nations Championship for home-based footballers, opened the scoring as Morocco overcame Uzbekistan 2-0 in Casablanca.
Victory for the Atlas Lions followed a win over Serbia in Turin and maintained impressive recent form under French coach Herve Renard.
After surprisingly winning in Poland, Nigeria disappointed when falling 2-0 to Serbia in London, where Aleksandar Mitrovic bagged a brace.
“We are a work in progress,” admitted Nigeria coach Gernot Rohr after a match controlled by the Serbs, who will not be going to the World Cup.
Senegal drew 0-0 with Bosnia and Herzogovina in French city Le Havre having also drawn with Uzbekistan in another World Cup warm-up.
In a match not involving World Cup qualifiers, Tanzania mocked the FIFA world rankings by beating the Democratic Republic of Congo 2-0 in Dar es Salaam.
Mbwana Samatta and Shiza Kichuya scored for the Taifa Stars, who are 107 places below the Leopards.
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