After two fighting draws, Anand did not achieve much in the opening as white, and once his position worsened Ivanchuk played in machine-like fashion to force a victory.
It was in fact a day of the underdogs in the Final Masters as World number one Magnus Carlsen of Norway also suffered a shock defeat at the hands of low ranked Francisco Vallejo Pons of Spain.
The other game of the category-22 event between Levon Aronian of Armenia and Hikaru Nakamura of United States ended in a draw.
After his second successive victory, Ivanchuk shot in to sole lead with seven points. Overnight joint leader Aronian, meanwhile, slipped to the second spot with five points, enjoying a two-point lead over nearest rivals Nakamura and Vallejo Pons.
Carlsen and Anand are currently languishing at the bottom of the tables with just two points that came from two draws in the first two rounds.
The 42-year-old Ivanchuk came to Sao Paulo after a gruelling World Cup that lasted three weeks, and so far he has maintained the high level that he showed there.