The 34-year-old former Liverpool star left it late in Cairo to overtake Hossam Hassan, scoring with a far-post header on 84 minutes and from a penalty five minutes into added time.
Hassan was fired as Egypt coach last week and replacement Ali Maher made a perfect start with goals from Nasser Maher, Omar Marmoush and Mohamed Hany building a 3-0 lead by half-time.
Egypt have seven points in Group B after three matches, three more than Angola, who host South Sudan on Saturday.
Achraf Hakimi, favourite to win a second successive African Footballer of the Year award next month, also bagged a brace as Group A pacesetters Morocco crushed Niger 5-1 in Casablanca.
Substitute Tolu Arokodaro scored twice within eight minutes as Nigeria beat Tanzania 3-1 in Uyo to get their campaign back on track.
Tunisia suffered a shock home 2-0 loss to Libya and Kenya scored in the final minute to snatch a surprise 2-2 draw away to South Africa.
Alhassan Yusuf put Nigeria ahead after just 103 seconds and Alphonce Msanga equalised on 32 minutes following a rare Tanzanian attack.
Arokodaro, scorer of six goals in his last five matches for Ajax Amsterdam, came off the bench for the second half and quickly made an impact.
His near-post back heel off a low cross put Nigeria ahead a second time after 52 minutes and as the match reached the hour mark, he struck again, with a close-range shot.
An ultimately comfortable victory lifted the Super Eagles to six points after three rounds in Group L, one point behind Guinea-Bissau, who drew 1-1 with Madagascar on Thursday.
Nigeria boost
Although bottom of the table with just one point, Tanzania are guaranteed a place at the 2027 AFCON as co-hosts with Kenya and Uganda.
That means Guinea-Bissau, Nigeria and Madagascar must fight for one place at the 24-nation tournament, the first to be staged in east Africa since Ethiopia were the 1976 hosts.
Nigeria were in trouble after a 3-0 hammering in Guinea-Bissau two months ago, but now have a clear path to a tournament they have won three times.
Away wins over Tanzania, on Tuesday, and Madagascar in March, and a home win over Guinea-Bissau, also in March, will assure qualification.
Tunisia are in Group H, which includes co-hosts and automatic qualifiers Uganda, and their record of reaching every AFCON tournament since 1994 is in peril.
A 2-0 defeat at home to neighbours Libya leaves them bottom of the table with just two points, and a venue switch two months ago means their remaining three fixtures are all away.
Ali Youssef converted a 44th-minute penalty for Libya and Hamdou Elhouni, who once played for leading Tunisian club Esperance, doubled the lead on 62 minutes.
Victory lifted Libya from last place to a share of the lead on four points with Uganda. Botswana and Tunisia have two each. Uganda host Botswana in Kampala on Saturday.
The Group D clash between South Africa and Kenya pitted two South African coaches against each other. Pitso Mosimane handles Bafana Bafana and Benni McCarthy guides the Harambee Stars.
Former Manchester United coaching staffer McCarthy was the happier at full-time after Ryan Ogam equalised in the final minute of regular time.
From a South African perspective this was two points lost, although they remain on top with seven. Guinea have six, automatic qualifiers Kenya two and Eritrea one.