The Proteas, chasing 312 to beat the tournament hosts at The Oval, suffered an early setback when Amla came off in the fourth over after a vicious short ball from England seamer Jofra Archer reared up and struck him.
Amla initially called for a new helmet to be brought to him from the dressing room but, after further inspection out in the middle, he left the field while rubbing his head and Aiden Markram came out to join Quinton de Kock.
South Africa were 14 without loss at the time, with Amla having made five from eight balls.
Markram lasted just 12 deliveries and was dismissed for 11 when he edged Archer to Joe Root at slip.
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