The third seed, playing her first clay tournament in almost three years after a two-year break to give birth to daughter Jada, had needed three sets to get past Alexandra Dulgheru on Wednesday and lost 7-5 4-6 6-4 to the little known Spaniard.
World number 10 Clijsters squandered three set points in the first set and broke serve twice in the third but left-hander Garcia Vidagany won 11 of the last 14 points to seal a memorable victory in her first appearance in a main draw on the tour.
Clijsters had ended American Venus Williams's 15-match winning streak with a 6-2 6-1 victory on hard court in Miami last week before flying across the Atlantic and switching surfaces for the tournament in southern Spain.
In another upset on Thursday, unseeded Italian Sara Errani knocked out seventh-seeded Spaniard Anabel Medina Garrigues, coming through 6-1 7-6.
Second seed Flavia Pennetta of Italy cruised past Spanish qualifier Laura Pous Tio 6-2 6-2 and top-seeded Bulgarian Victoria Azarenka takes on another Spaniard, wildcard Estrella Cabeza Candela, later on Thursday.