Gaviria easily outsprinted German Ruediger Selig (Bora Hansgrohe) and Italian Giacomo Nizzolo (Trek Segafredo).
"We knew there were come crosswinds near the finish so we wanted to split the peloton there," said Jungels.
With about 10km left, a brutal acceleration by Quick Step-Floors split the peloton and all the pre-race favourites were trapped behind, leaving a front group of eight to fight it out for the stage win after 148km between Tortoli and Cagliari.
Overall, Gaviria leads German Andre Greipel (Lotto Soudal), who started the day in pink, by nine seconds.
Monday is a rest day and Tuesday's fourth stage will end on the flanks of Mount Etna, where the pre-race favourites such as defending champion Vincenzo Nibali (Bahrain-Merida) and 2014 winner Nairo Quintana are expected to play their first cards.
(Reporting by Julien Pretot,; Editing by Pritha Sarkar)
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