Egypt reached the semi-finals of Afcon 2025 and the last 16 of this year’s Fifa World Cup under Hossam Hassan but parted company with the 60-year-old earlier this month.
The Pharaohs had taken four points from their opening two games in Group B, with Salah substituted after an hour in their 0-0 draw with Angola before missing the win in South Sudan.
The former Liverpool forward returned as captain against Malawi, and Egypt cruised into a 3-0 lead at the break through goals from Nasser Maher, Omar Marmoush and Mohamed Hany.
Salah got on the scoresheet when he stooped to head in a cross from the left and rounded off proceedings by dinking in a penalty after Hamza Abdelkarim was tripped in the box.
Victory in Maher’s first game at the helm puts Egypt three points clear of Angola, who take on South Sudan on Saturday.
In Group A, Morocco had also looked like they would ease to three points against Niger in Casablanca after Yassir Zabiri’s early effort and a brilliant long-range strike from right-back Hakimi put them 2-0 up after 27 minutes.
But Mohamed Abdourahmane headed in to halve the deficit and Niger had a chance to level from the spot on the stroke of half-time after a handball by Noussair Mazraoui.
However, Atlas Lions goalkeeper Bounou moved to his left to keep out Youssouf Oumarou’s penalty, and Hakimi made it 3-1 in first-half stoppage time with a dipping free-kick from distance.
Youssef En-Nesyri steered in the fourth in the 77th minute from a Hakimi pass and Ayoub Oufkir completed the scoring from close range in the final minute.
Earlier in Group A on Friday Gabon beat Lesotho to move on to six points thanks to two second-half goals from Denis Bouanga.
The LA FC forward smashed the right-hand upright with a penalty but broke the deadlock with a header a minute later and then scored from 12 yards when the Panthers were awarded a second spot kick.