After a touchline fracas that saw Santos boss Cuca sent off, Breno – who replaced Gabriel Menino in the 85th minute – rose highest at the back post to nod a sensational right-wing delivery from Rony back across goal and into the far corner.
It was Rony's 13th goal involvement (five scored, eight assisted) in this season's Libertadores and it settled what had been a drab game of few chances in front of a small crowd.
Palmeiras were consequently crowned Libertadores champions for the second time in their history, with Abel Ferreira becoming just the third European coach to lead a team to glory in the competition.
Despite a fiery start there was minimal tempo in the play of both sides, with the temperature in Rio de Janeiro over 30 degrees Celsius at kick-off.
Raphael Veiga dragged the best opening wide before half-time and 14 minutes after the restart Lucas Verissimo nodded a free-kick from Marinho narrowly off target.
Veiga thundered a free-kick just over after the hour mark and Felipe Jonatan flashed a half-volley wide before Cuca was shown a red card in stoppage time for trying to stop Marcos Rocha taking a quick throw-in.
Santos were seemingly distracted by the incident and Palmeiras punished them, with Breno getting above Para – a champion with Santos in 2011 – to head home the decisive goal without the need for extra time.