The teams drew 1-1 in the first semifinal at Chile last week.
Sao Paulo dominated the match in front of nearly 60,000 fans at its Morumbi Stadium.
Universidad Catolica had a couple of chances with balls crossed into the area in the final minutes, but could not capitalize on the opportunities.
Sao Paulo—led by Luis Fabiano, Lucas and Paulo Henrique Ganso—will play the final of the South American competition against either Millonarios of Colombia or Tigre of Argentina, who face play other Thursday in Colombia following a 0-0 draw in the first leg.
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