World No. 68 Andujar took full advantage of Thiem's lapses in concentration on way to upsetting the 2018 and 2019 finalist in over four hours and 28 minutes on Court Philippe-Chatrier.
Andujar, who beat Roger Federer at the Gonet Geneva Open two weeks ago, now has a 6-23 career record against top 10 opponents.
Andujar will now play either Moldovan Radu Albot or Federico Delbonis of Argentina.
World No. 4 Thiem, who finished as runner-up to Rafael Nadal in the 2018 and 2019 finals, is now 9-8 this season. This was his first opening-round loss at Roland Garros in eight appearances.
In other action, Italian No. 27 seed Fabio Fognini struck 31 winners in a 6-4, 6-1, 6-4 win over French wild card Gregoire Barrere in two hours and eight minutes.
Fognini now plays Hungary's Marton Fucsovics, who beat Gilles Simon of France 6-4, 6-1, 7-6 (5) over three hours and 13 minutes.
British No.1 Dan Evans's search for a maiden French Open title will continue after he went down to 21-year-old Serbian Miomir Kecmanovic 1-6, 6-3, 6-3, 6-4 in the first round. This was the 27th ranked player's fourth time in Roland Garros main draw and he is yet to make it through to round two.
Paris, May 31
Spaniard Pablo Andujar made a remarkable recovery from being two sets down, for the first time in his career, to beat a top-5 player when he shocked fourth seed Austrian Dominic Thiem 4-6, 5-7, 6-3, 6-4, 6-4 in the first-round of French Open on Sunday.
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