The Palace frontman netted twice in the second-half to hand his country a 2-1 victory, with the Swiss taking the lead just 12 minutes in.
Completing the full 90 minutes, Batshuayi bagged his 20th and 21st international goal from just 32 games. Five of these efforts have come from three matches in 2020, taking the forward's international tally as an Eagle to four from five across his two spells.
He earned Belgium's 'Devil of the Match' for his game-winning performance against Switzerland.
On the same night, fellow Red Devil Christian Benteke was an unused substitute, with clashes against England and Denmark still to play.
Cheikhou Kouyate also enjoyed international acclaim on Wednesday as he captained Senegal to a 2-0 victory over Guinea Bissau. The Palace No.8 helped lead his side to an Afcon qualifying win after Sadio Mane netted from the spot and then assisted Opa Nguette in the 74th-minute.
Elsewhere, Patrick van Aanholt returned to the global stage but remained on the bench as the Netherlands drew with Spain.