Alerrandro opened the scoring for Atletico two minutes before the break with a goal that was validated after consultation with the Video Assistant Referee.
Former AC Milan striker Pato fired home the equaliser 27 minutes into the second half.
Atletico are fifth on 16 points after nine games while Sao Paulo sit ninth on 14.
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(Reporting by Andrew Downie; Editing by Peter Rutherford)
