Santos' opener six minutes into the second half, a superb goal by 20-year-old Ganso from outside the box into the top corner of Victor's net, calmed their anxious fans at the Vila Belmiro by putting them level 4-4 on aggregate.
Robinho scored the second with a fine lob over Victor 20 minutes from time and after defender Rafael Marques pulled one back, midfielder Wesley secured victory by dribbling past the keeper to score the third five minutes from time.
In the dying minutes both teams were left with 10 men when Santos defender Edu Dracena and Gremio striker Jonas were sent off for fighting. Gremio then had Marques dismissed for a second booking after a violent foul on substitute Marcel.
Santos, who won the Paulista (Sao Paulo) state championship earlier this month, will meet Vitoria in the Copa Brasil final. Vitoria beat Atletico Goianiense 4-0 at home on Wednesday and 4-1 on aggregate.
The final, with a Libertadores Cup berth at stake, will be played after the World Cup, the first leg on July 28. The second leg on Aug. 4 is the final day of Robinho's loan from Manchester City.
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