At least three union members were injured in the Sao Paulo clash, said Paulo Iannone, a union spokesman.
Operators of the subway and overland trains were in the second day of a strike for higher wages, with no indication that it would end soon. Late on Friday, officials and the union representing workers said they had not reached an agreement to end the strike and it would continue into Saturday.
That's worrying for authorities because most fans heading to Thursday's opening Cup match in Sao Paulo will need to use the subway.
Cup organisers have fretted for a year that a resurgence of mass anti-government protests could mar the game's premiere event, with all the world watching. But in recent weeks, a series of strikes by public transport workers, police, teachers and others in several Cup host cities has proved more disruptive than demonstrations.
If such strikes continue, ''there will be chaos during the World Cup,'' said Carla Dieguez, a sociologist at Sao Paulo University's School of Sociology and Politics. ''What we don't know is how long the (subway) strike will last and if workers in others cities where games will be held will also go on strike.''
Unions across Brazil are using the leverage of the World Cup in an effort to get concessions from authorities, as has happened before other big sporting events. Ahead of South Africa's World Cup in 2010, bus drivers went on strike. So far, it's often worked, as in the case of federal police officers and garbage collectors in Rio de Janeiro who have won better wages recently.
Unions argue that high inflation is eating away at workers' purchasing power. On Friday, the government statistics agency said the benchmark consumer price index rose 6.37 percent in the 12 months through May.
Justice Minister Jose Eduardo Cardozo made an appeal to national pride to get strikers to return to work in time for the Cup.
''We want to feel proud of our country,'' Cardozo said. ''On and off the pitch we must show what we are capable of.''
Unions in Brazil are strong and often strike to demand higher wages and better working conditions.
Brazil's former President Luiz Inacio Lula da Silva got his start as a fiery steel workers union leader who led massive strikes that weakened Brazil's military dictatorship. Silva went on to start the ruling Workers Party, which has strong ties to unions, though they've often been strained since the party took the presidency in 2003.
It's not just Sao Paulo that's seeing union action. Striking teachers in Rio de Janeiro blocked main roads during Thursday's evening rush hour, snarling traffic.
A two-day walkout in April by state police officers in the northeastern World Cup host city of Salvador led to a spike in homicides and robberies. One week earlier a police strike in the city of Fortaleza, also a World Cup host, brought widespread looting during two days.
Last month, a 48-hour strike by Sao Paulo and Rio de Janeiro bus drivers left hundreds of thousands of people unable to get to and from work, while civil police in 14 states went on a 24-hour work stoppage demanding higher wages. The police strike affected at least six cities that will host World Cup games: Rio de Janeiro, Sao Paulo, Salvador, Manaus, Recife and Belo Horizonte.
Federal police agents, who oversee immigration at international airports, and state police officers responsible for keeping order on the streets have said they may strike during the World Cup despite an injunction from the Supreme Court ordering them not to halt work during the tournament.
The authorities and courts haven't shown any ability to force public workers in services essential to the World Cup to show up for their jobs.
A judge had ordered Sao Paulo's train operators to work at full capacity during rush hours and at 70 percent capacity in off hours. Union members voted to go ahead with the strike anyway, disdaining the judge's order that the union be fined $44,000 each day it ignores the ruling.
The union said on its website the strike would continue until officials met its demand for a pay hike of at least 10 percent. The Sao Paulo state government company that runs the subway system has offered an 8.7 percent increase.
The strikes have overshadowed earlier worries about disruptions from protests fed by anger over the billions spent to host the World Cup while Brazil's schools, health system and public transit have widespread problems.
Last year, huge protests took over streets in dozens of cities during the Confederations Cup. On just one night, a million people were out in the streets across Brazil to join in demonstrations. Violent clashes between young protesters and police erupted at many of last year's protests, and threats by some groups to organize demonstrations during the World Cup raised concerns about security during the tournament.
But while there have been almost daily protests in the weeks before the tournament, the marches have been far smaller than a year ago.
The subway strike in Sao Paulo illustrated the potential for disruptions during the World Cup. The more than 3.5 million people who use the city's public transit systems on weekdays faced chaos as only three of the five subway lines operated, and with limited service.
''It is opportunism. They want a pay raise and are using the World Cup as a tool,'' said Pedro Araujo, an annoyed truck driver. ''Yes, we want to fight for our rights and for what is fair, but not like this, affecting everyone.''
Associated Press writers Bradley Brooks in Rio de Janeiro and Adriana Gomez Licon in Sao Paulo contributed to this report.