The 17-year-old, who agreed to join Arsenal for a reported free of 10 million reais in December, came on as a late substitute and set up Mariano for the winning goal with a brilliant run in the 83rd minute.
The forward, making his fifth first team appearance for Fluminense, will join Arsenal when he turns 18 in January 2011.
Botafogo, winners of the first of two stages in the championship, went in front against the run of play with a penalty converted by Argentine forward German Herrera eight minutes before half time.
Former Olympique Lyon striker Fred scored a deserved equaliser with a volley on the hour in the match at the Maracana.
However, Fluminense found themselves under pressure from the 68th minute when their Argentine forward Dario Conca was shown a straight red card for a foul on Botafogo captain Lucio Flavio.
Botafogo, who had gone eight matches unbeaten in the Rio championship, were then also reduced to 10 men in the 77th minute with Herrera's second booking.
Wellington, discovered by Arsenal manager Arsene Wenger during a European tour by a Fluminense junior team in 2008, could have scored near the end but his shot after an exchange of passes with Fred was just wide.
"I can't say I'm ready, I've still got a lot of work to do," the Brazil under-17 international said.
"I don't like to talk too much about Arsenal, I'm at Fluminense and I love this club. I know it's many players' dream (to play in Europe) and I'm no different but I owe Fluminense a lot and I'll always remember this club."
Carioca title holders Flamengo, playing without Brazil striker Adriano after he was dropped for missing Friday's practice, cruised to a 4-0 win over Resende on Saturday as they build up to Wednesday's Libertadores Cup match at FC Caracas.
