"Pique started the session but just after the halfway point he withdrew," the Spanish soccer federation (RFEF) said on the team's website (www.sefutbol.com).
"The federation's medical team will assess the extent of the injury," they added.
Reserve goalkeeper David De Gea, who also has a muscle injury, missed training completely, while the other 21 members of the squad are available for the clash in Curitiba, the RFEF said.
Holders Spain are looking to end their campaign at the finals in Brazil with a victory after they were eliminated from the tournament thanks to resounding defeats to the Netherlands and Chile in their opening two matches.
Pique had a poor game against the Dutch and coach Vicente del Bosque dropped him for the Chile match, bringing Javi Martinez in to partner Sergio Ramos at centre back.
Raul Albiol, who has yet to feature in Brazil, is another option in the middle of the defence.
He told a news conference on Saturday Spain faced a period of transition.
Stalwarts like midfielders Xavi and Xabi Alonso and forwards Fernando Torres and David Villa will likely retire from international football before the European champions defend their title at Euro 2016 in France.
"After a World Cup there are always players going and others coming in," Albiol said.
"There is time and little by little each team mate will make the decision they have to make."
Australia are also out after they were beaten 3-1 by Chile and 3-2 by the Dutch in their two outings.
"I would like to have played with something still up for grabs but we are playing for the pride of winning a match at this World Cup," Albiol said.
"Every match should be exciting, even if it's a friendly in Vietnam. We have to go off on holiday with positive feelings."
(Writing by Iain Rogers in Brasilia, editing by Justin Palmer)
