The South African Rugby Union announced the news on Tuesday night.
The Springbok lock was cited for allegedly making contact with the "eye or eye area" of Scotland fly-half Greig Laidlaw in the second half of Saturday's 21-10 victory at Murrayfield.
The South African Rugby Union announced the verdict on their official Twitter page, saying: "Good news on Eben Etzebeth - he's not guilty and free to play against England on Saturday."
Etzebeth, 21, appeared before the independent judicial officer, David Martin, who ruled the contact with Laidlaw's eyes was accidental.
An official statement from the Six Nations, who oversee disciplinary matters in the autumn internationals, read: "The judicial officer held that the contact in the area of the Scotland player's eyes was accidental, and as such did not constitute foul play.
"Eben Etzebeth is free to resume playing immediately."
The South Africa team to play England at Twickenham on Saturday will named by head coach Heyneke Meyer tomorrow morning.
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