Campaigners said a long legal process lay ahead as both the government and its commercial partners would likely appeal the court ruling. Analysts said work on the $11 billion dam, which would be the third largest in the world, could be delayed but was unlikely to be abandoned because of the powerful pro-dam players involved in the project.
Initial construction work along the dam's site on the Xingu River, a tributary of the Amazon, began a year ago despite fierce opposition from Brazil's green movement and its supporters worldwide, including a strong lobby led by Hollywood film director James Cameron.
The court's suspension order observed that indigenous communities weren't properly consulted before President Dilma Rousseff's government gave a go-ahead to the project last year.
Rousseff has made known her support for the dam as well as other projects that may involve the loss of Amazonian fauna and flora. Critics say the president is giving priority to short-term economic gain over long-term interests of the Amazon region's rich resources.
Environmentalists warn of deforestation, greenhouse-gas emissions and irreparable damage to the ecosystem.
Estimates of the native population the dam will displace vary, ranging from 20,000 to 40,000 people as large areas of established communities are submerged.
Controversy over the dam flared in 2005 when the Brazilian Congress approved the project.
The court noted that when congress approved the project in 2005, it called for an environmental impact study after the start of the work.
Native communities were given the right to air their concerns in parliament on the basis of that environmental-impact study. This wasn't done, the court said.
The Xingu Vivo indigenous movement hailed the court ruling as a "historic decision for the country and for the native communities." The judgment proved that "Belo Monte is not a done deal." Environmentalists and activists in Brazil's green movement are less optimistic and remain convinced the dam will be built.
About 150 indigenous activists recently occupied one of the dam's four construction sites for three weeks to demand that Norte Energia honor commitments made to their communities.
The federal government in Brasilia says it will spend more than $1.2 billion to assist those likely to be displaced by the dam.
Norte Energia, the construction company running the project, faces fines of $250,000 a day if it chooses to ignore the ruling but it can appeal in a higher court.
Due to be operational by 2014, the dam is designed to produce more than 11,000 megawatts of electricity which the government argues is vital for Brazil's industrialization. When completed, the dam will only be surpassed in size by China's Three Gorges dam and the Itaipu hydro-electric complex, which is shared by Brazil and Paraguay.