His stoppage-time dismissal capped an afternoon in which Botafogo were also awarded a penalty, only for the referee to change his mind as Seedorf was about to take the kick.
The first-half spot-kick was awarded with the game still goalless when Rafael Marques appeared to be fouled in the penalty area.
Former AC Milan, Ajax, Sampdoria and Real Madrid midfielder Seedorf had began his run-up when the referee stopped the game, consulted his linesman and changed his mind, saying that Marques had been passed the ball by a player in an offside decision.
Botafogo protested angrily, claiming the referee had received information from sources off the pitch who had seen television replays.
On being substituted at the end, Seedorf, who scored the winning goal in the 68th minute, walked towards the Botafogo bench but was ordered by the referee to go off on the other side of the pitch to save time,
Seedorf protested, was booked, turned his back on the referee and was given another yellow card.
"I didn't understand anything," he told touchline reporters.
The game was played in the Carioca championship, one of a plethora of regional tournaments which kick off the Brazilian season.
The weekend's programme went ahead as usual even though some clubs were missing players called up for Brazil's friendlies against Italy, which they drew 2-2 in Geneva last Thursday, and Russia in London on Monday.
Brazilian champions Fluminense, missing three players including striker Fred, drew 0-0 at Duque de Caxias in front of barely more than 1,000 fans on Saturday.
Santos, deprived of prodigy Neymar, drew 0-0 with Palmeiras in the Paulista championship on Sunday. (Reporting by Brian Homewood)
- Sports & Recreation
- Rafael Marques