Palmeiras secured a 1-1 draw at Coritiba's packed Couto Pereira stadium after winning the first leg 2-0 last week in Sao Paulo to give Scolari his fourth Copa Brasil as a coach.
Substitute Ayrton had put Coritiba ahead with a majestic free-kick just after the hour mark, but striker Betinho headed home the equaliser from midfielder Marcos Assuncao's cross in the 66th minute.
"A team like this should be an example for the history of Palmeiras," said Scolari after his players had poured drinks over his head in celebration.
"In these two years so much has been experienced by all of us ... a title at this moment comes as a reward to an entire group," he added.
Former Brazil, Portugal and Chelsea coach Scolari returned to Palmeiras in 2010 after his first successful spell at the club from 1997-2000.
Since guiding Brazil to World Cup victory in South Korea and Japan in 2002, he had won only the Uzbekistan league title with Bunyodkor in 2009.
The victory means Palmeiras is the second Brazilian team to qualify for next year's Copa Libertadores, after arch rivals Corinthians clinched the South American championship title last week.
It was Scolari's fourth Copa Brasil win after success in 1998 also with Palmeiras and 1994 (Gremio) and 1991 (Criciuma).
Coritiba were also beaten in last year Copa Brasil final to Vasco da Gama.