The Pharaohs, who have not conceded in two victories over Libya under Queiroz, were taken aback after falling to a goal from Valencia striker Helder Costa and a penalty from M'Bala Nzola.
However, Mohamed Salah inspired a comeback when he set up Mohamed Elneny for Egypt's first goal on the stroke of halftime before providing another assist for right-back Akram Tawfik 14 minutes into the second half.
Egypt were lethargic and porous in the first half but regrouped after the restart to avoid what would have been their first defeat under Queiroz.
The Portuguese blamed humidity and hot weather for the poor first-half display but credited his men for staging a superb comeback.
"Two things happened in the first half -- the humidity and the hot weather. This cost us a lot of time to adapt to the conditions," Queiroz told OnSport in a pitch-side interview following the match.
"We started flat to adapt to the humidity and the warm environment. It was difficult for our team.
"Unfortunately we conceded two goals in that period, but the reaction was fantastic. When we started to control the midfield, things changed. We scored two goals and we should have won this game.
"It's not easy to be losing 2-0 and have this great reaction. Everybody must be proud of the players," he added.
Egypt, who are on top of their group with 11 points, gained an unassailable four-point lead over second-placed Gabon, who defeated Libya (six points) 1-0 earlier in the day. Egypt and Gabon meet in a dead-rubber on Tuesday.
The team will feature in the inaugural FIFA Arab Cup in December before taking part in the African Nations Cup in Cameroon a month later.
While Queiroz acknowledged the importance of doing well in both tournaments, he said his ultimate task is to qualify Egypt for the World Cup.
"Our minds must be on the World Cup during the Arab Cup. We use the opportunity to put new players on the pitch," he said.
"We also of course need to try to win every single game at the African Nations Cup, but it's important to make everybody understand that my job and my goal is the World Cup."
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