Rigoberto Uran (Cannondale-Drapac), George Bennett (LottoNL-Jumbo) and Serge Pauwels (Dimension Data) were all initially penalised 20 seconds for taking drinks from the side of the road within the last 20km, before the commissaires reversed their decision ahead of stage 13.
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A UCI statement said that the eventual decision not to penalise the riders was taken because riders were unable to take food and drink earlier in the race.
Watch: Tour de France stage 12 highlights
“In light of the inability of teams to resupply their riders before the last climb of stage 12 of the 2017 Tour de France due to specific circumstances of the race which had blocked vehicles, the UCI Commissaires Panel has decided to annul the penalties imposed on riders Serge Pauwels, George Bennett and Rigoberto Uran,” the statement read.
The original decision had been the subject of controversy after footage emerged of eventual stage winner Romain Bardet taking a bottle from a spectator at the same time as Bennett, but escaping punishment.
The race continues on Friday with a 101km stage from Saint-Girons to Foix.