The JiR rookie mastered the treacherous wet conditions to post a best lap of one minute 54.463 to hold off Interwetten-Paddock's Thom Luthi by just three hundredths of a second.
Speed Master's Andrea Iannone was third quickest, a further two tenths back.
Mike Di Meglio, Yuki Takahashi and Max Neukirchner all fell off in the wet, cold conditions.
The Estrella Galicia rider shrugged off wet and cold conditions as he clocked a best lap of one minute 58.316 seconds in Jerez to finish ahead of Red Bull KTM's Arthur Sissis.
Oliveira's team-mate Danny Kent was third fastets, just two hundredths further back.
Title favorite Maverick Viñales spent much of the session in the pits, setting only the 11th fastest time of the day.
The conditions took their toll on the competitors, however, with riders including Isaac Viñales, Giulian Pedone, Alan Techer, Kenta Fujii and Jack Miller all coming off in the final quarter of an hour.