Sangakkara was pulled up by match referee Alan Hurst after he collided with Black Caps' bowler Nathan McCallum while turning for a second run during Friday's match in Dambulla.
Hurst charged Sangakkara with a Level 2 offence of the International Cricket Council's Code of Conduct which relates to "inappropriate and deliberate physical contact between players in the course of play."
But the former Australian fast bowler let off the Sri Lankan captain after examining video evidence of the incident.
"I looked at video footage of the incident from various angles and considered the detailed evidence of the umpires," Hurst said in an ICC statement.
"I found that video evidence that was put forward by the player provided reasonable doubt as to whether the contact was deliberate.
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The match was abandoned due to heavy rain with Sri Lanka, sent in to bat, on 203-3 from 43.4 overs.
Sangakkara was ticked off by Sri Lanka Cricket on Wednesday for another incident when off-spi