The Olympic silver medallist jumped 15.43m, adding seven centimetres to Tatyana Lebedeva's old mark which had stood since March 2004.
It was two centimetres better than her lifetime outdoor best, and some 40 cm better than her previous indoor personal record before the meet.
The record is subject to World Athletics' ratification processes.
Only one woman has ever jumped further, indoors or outdoors.
That is Ukraine's Inessa Kravets, the (outdoor) world record holder at 15.50m, a mark that is 25 years old this year.
Rojas was born two months after Kravets, the Atlanta 1996 Olympic champion, set that record in August 1995.
The 24-year-old opened her competition in Madrid with two fouls in her first three jumps, but her fourth of 15.29m was enough to break her own South American indoor record set earlier this month.
She then fouled her fifth before producing the record leap on her sixth attempt.