Police in Sao Paulo said they had apprehended around 200 flip-flops which Palmeiras fans had intended to throw at their own team while a group of Guarani fans stoned their club's offices after the team were relegated.
Television pictures showed trouble erupting after relegation-threatened Botafogo were beaten 2-1 at home by Corinthians at the Caio Martins stadium in Niteroi near Rio de Janeiro.
Several fans invaded the pitch one attempted to attack the referee and was kicked by a linesman as he was restrained by police.
Fans behind one goal attempted to break down the fencing and fought with police who went onto the terraces to restore order.
Truncheon-wielding police were also seen fighting with supporters some covered in blood outside the stadium.
There was also trouble at Vasco da Gama's notorious Sao Januario stadium in Rio de Janeiro.
Witnesses said that hundreds of Atletico Paranaense fans who had made a 12-hour coach journey from Curitiba in the hope of watching their team wrap up the title were denied entry to the ground despite holding tickets.
Media reports said fans hurled bottles and stones at police after the gates were closed.
Police also stopped a further 14 coachloads of fans from approaching the stadium to prevent trouble from escalating.
Angry Paranaense supporters showed their tickets to television cameras as the buses were forced to wait in an industrial area on one of the main roads into the city.
Inside the ground Paranaense players complained they were not allowed to warm up on the field.
Paranaense who would have clinched the title if they had beaten Vasco and Santos had lost were knocked off the top after they lost 1-0 and Santos beat Sao Caetano 3-0.
Palmeiras players were spared being pelted with flip-flops after police discovered that the organised supporters group known as the Mancha Verde (Green Stain) was planning the protest after the match at home to Criciuma.
The flip-flops were confiscated before the match. Supporters said they had symbolised the 'sandals of humility' which they suggested the players needed to wear.
Guarani who were condemned to second division football when they lost 4-2 to Paysandu announced they would play their remaining home game against Gremio at a neutral venue to avoid possible protests by their own fans.
Around 20 fans broke windows at the club's headquarters in the city of Campinas after pelting it with stones on Saturday night.