The Teranga Lions came into the tournament as one of the favourites, and while they progress to the next stage at the top of their group with five points, it was by no means convincing.
Malawi looked to carry the greater threat in the first half, with Gabadinho Mhango seeing a couple of long-range efforts go close.
Senegal did at least test Charles Thom in the Malawi goal early in the second half, with Abdou Diallo's header tipped just over, though it was hardly a sign of imminent domination.
Malawi then looked set to take the lead with 15 minutes left when Bouna Sarr conceded a penalty for appearing to foul Gomezgani Chirwa, but the decision was overturned after a VAR check, much to the Flames' fury.
As a result, Senegal finished top of the group, meaning it will play one of the best third-placed teams, while Malawi finishes third behind Guinea by virtue of an earlier defeat to them.