The first-ever match between these two countries in AFCON proved to be a feisty encounter that only came to life in the second half.
Senegal started on the front foot and had the best chance of the first half as a cut back from Idrissa Gueye found Sadio Mane but the Liverpool star skied his effort wide from 12 yards.
Malawi also came close through Mhango Gabadinho and left-back Gomezgani Chirwa, who had a brilliant outing for the Flames. The first half ended with nothing to separate the two nations.
In the second half, it was all Senegal as the Teranga Lions dominated and created the best chances but were denied each by the Malawi goalkeeper, Thom.
The 25-year-old made three excellent saves, twice he denied Habib Diallo three minutes after the restart and then 10 minutes.
Five minutes later, Thom pulled off another save to deny Gueye from a free-kick and then another late save to earn his country a crucial point.
Senegal finishes top of the group despite the result after Zimbabwe shocked Guinea in the other Group game, while Malawi's Flames stay third on four points.
The Teranga Lions advance to the knockout stages as group winners, alongside Guinea's Syli Nationale, who finished second despite a shock defeat to the Warriors of Zimbabwe.