Habib Diallo and Sadio Mane went close for Senegal, while Malawi had the award of a penalty overturned following a video assistant referee review.
The Flames thought they had a spot-kick in the 74th minute when left-back Gomezgani Chirwa went down under the challenge of Bouna Sarr.
But referee Blaise Yuven Ngwa reversed his decision after studying replays.
Malawi finish third in the table on four points and could yet qualify for the last 16 in Cameroon as one of four best-ranked third-placed sides.
Senegal, Nations Cup runners-up in 2019, only scored one goal in their three group matches – Mane’s 97th-minute winner against Zimbabwe in their opener.
The Teranga Lions will face a third-placed side from Group A, C or D in the last 16 on Tuesday, 25 January.