The Proteas were 159-2 in the 28th over, with De Kock having struck 92 off just 76 balls, including 13 fours, when rain stopped play for the second time in the match at Headingley.
Both sides needed to bat for a minimum of 20 overs for a result to be declared under the Duckworth-Lewis-Stern method for rain-affected white-ball games.
But the umpires deemed that would not be possible when they called the game off shortly after 4:00 pm local time (1500 GMT) as a series that had started during a nationwide heatwave ended in more familiar English conditions.
The abandonment meant left-hander De Kock was just eight runs shy of what would have been his 18th ODI century. England had gone into the game looking to avoid a third consecutive white-ball series defeat under new captain Jos Buttler, who succeeded now retired 50-over World Cup-winning skipper Eoin Morgan, following T20 and ODI reverses against India.