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.
Ivanchuk had finished third in the World Cup, which gave him a seat in the next world championship cycle.
It was not Anand's day as the Ukrainian went for the Jaenisch variation in the Ruy Lopez that is recently gaining momentum thanks to the exploits of Azeri Teimour Radjabov.
The middle game saw Anand allowing an easy equality and then Ivanchuk came on top with thematic central breakthrough.
Anand reached a queen and minor piece endgame after losing a pawn and that was enough for Ivanchuk to force matters.
Towards the end, Anand found many resources but Ivanchuk displayed excellent skill and patience to romp home in 69 moves.
Carlsen was quite unlucky as he let go a won position against Vallejo. Starting off with a Pirc defence, Carlsen did everything right for the major part of the game and gained space with some finely crafted manoeuvres.
Pons fell under time pressure too and it looked all over for the Spaniard when suddenly Carlsen dropped a piece and had to resign after 42 moves.
"I got a pleasant position from the opening. He probably played inaccurately at some point. It became huge, almost wining advantage. At one point I wasted too much time trying to find a forced win. Then I... blundered a piece very simply. I don't know if you can call it an optical illusion or whatever," Carlsen said after the game.
Aronian and Nakamura discussed the intricacies of a Slav Fianchetto where the former played black. Maintaining a level position for a long time, Nakamura eventually signed peace after 46 moves.