Uran had been sanctioned for taking a bottle from a Cannondale staffer inside the last 10 km of Thursday's stage.
Explaining its decision, the UCI said teams were unable to feed their riders earlier because of traffic.
"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 (Team Dimension Data), George Bennett (Team Lotto NL - Jumbo) and Rigoberto Uran (Cannondale Drapac Pro Cycling Team)," a UCI statement said.
Uran stays fourth in the overall standings, 35 seconds behind race leader Fabio Aru and not 55 seconds off the pace as was the case before the reversal of the penalty.
TV footage showed stage winner Romain Bardet, who is third overall, grab a bottle from a spectator 6.4km from the line.
(Reporting by Julien Pretot; editing by Mark Heinrich)
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