Andressa Alves scored from close range in the 44th minute after a miscued clearance off the line went straight to the striker.
Spain's Irene Paredes hit the post in second-half injury time, a moment of rare excitement in a game notable for a flurry of missed passes and some wayward shooting.
Spain did not have one shot on target.
Brazil have six points from two games and are through to the next round along with Group C leaders Japan. Spain have one point and Costa Rica and South Korea, who play later on Saturday and also have one point, cannot both catch the South Americans.
Seventh-ranked Brazil struggled to a 2-0 win over South Korea in their first match and showed the same lack of sharpness against Spain. Veteran striker Marta, who scored a record 15th World Cup goal in the first game, made virtually no impact.
The match in the cavernous Olympic Stadium was played before a much larger crowd than the 10,000 crowd at the opening games.
(Reporting by David Ljunggren; Editing by Ken Ferris)
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