In a daring predawn raid yesterday, South African commandos crossed into the capital of neighboring Mozambique and destroyed the headquarters of their black nationalist guerrilla foes, killing at least six people, according to news agency reports from Johannesburg.

The raid on facilities of the South African National Congress in the suburbs of Maputo marks the first time South African military forces have struck into Mozambique, a country with which Pretoria has economic, transport and trade ties despite the Mozambicans' support for the nationalists.

South African military chief Constant Viljoen justified the raid by saying his government had received "irrefutable information" that the congress facilities in Maputo were being used as a "springboard for terror against South Africa."

Viljoen cited attacks in the first half of last year on South African police stations, a fuel manufacturing plant and a bank as examples, saying the attacks had been planned and launched in Maputo with assistance from the Palestine Liberation Organization and East German and Cuban advisers.

The military action appears to indicate a more aggressive stance by Pretoria against the congress and the countries giving it sanctuary. It comes only two days after Secretary of State Alexander Haig advocated a new U.S. get-tough policy toward what he called "rampant international terrorism."

An Israeli defense spokesman Thursday specifically cited the new U.S. policy, drawing on comments by President Reagan, in justifying heavy retaliatory raids against Palestinian targets in southern Lebanon following a rocket attack on an Israeli town by the Palestinians.

South Africa's raid early yesterday is in sharp contrast to its attitude a year ago when several incidents by congress insurgents, who had infiltrated into South Africa from Mozambique, provoked a severe diplomatic protest to the Marxist government of Samora Machel, but no military retaliation.

In addition, guerrilla infiltration from Mozambique fell off significantly in the last half of 1980, if reported incidents can be regarded as evidence of the guerrilla presence inside South Africa.

The congress, which opposes apartheid and is outlawed in South Africa, is the country's oldest black political organization. It adopted a policy of military action to overthrow white minority rule 20 years ago after it was banned by the South African government. It is financed and armed by the Soviet Union.

The unprecedented strike is sure to sour relations between South Africa and Mozambique, whose government is already being increasingly harassed by attacks from an antigovernment guerrilla movement that is supplied and supported by South Africa, according to several sources in both countries. The Mozambique Resistance Movement reportedly has increased its activity in recent months, causing embarrassment and annoyance to Machel's government.

According to news agency reports from Maputo, Mozambique's deputy defense minister, Lt. Gen. Armando Guebuza, condemned the raid as "a foul and criminal act." He said it was a challenge to Mozambique's right to shelter South Africans "being persecuted by the apartheid regime."

The South African military communique announcing yesterday's raid said that three "planning and control headquarters" of the congress were destroyed and "numerous terrorists" killed. The government-run Mozambican News Agency reported that six congress members, one South African soldier and one civilian, a Portuguese national, were killed in the raid.

The South African announcement mentioned no casualties among South African forces, but news agencies quoted one diplomatic source in Maputo as saying he had seen the body of the South African soldier.

One house was located in the seaside suburb of Matola, 10 miles northeast of Maputo and 40 miles from the South African border. One agency report said the South African forces arrived by helicopter in the Mozambican capital. The diplomatic source also said the South Africans used mortars, rockets and automatic weapons in the attack.

The South African raid appears to indicate that Pretoria is not going to shrink from actively engaging the congress guerrillas on its northeast border even though it is already fighting with another guerrilla movement in the territory of Namibia (South-West Africa) on its western border.

South Africa passed up an opportunity to put an end to that conflict during a recent conference in Geneva held under United National auspices. Although the black guerrilla organization, SWAPO (South West Africa Peoples Organization), said it was willing to accept a cease-fire, the South Africans said any plan for a cease-fire and elections leading to independence in Nambia would be "premature."

The South African action yesterday also follows the announcement this week by Prime Minister Pieter W. Botha that elections would be held in April. Botha's ruling National Party will easily win a new mandate from its whites-only constituency, but the leader will be fighting a rear-guard action during the campaign against a vociferous right wing that regards him as too conciliatory to blacks.

Yesterday's raid, as well as the announcement two days ago that the South African police had captured a Soviet spy, are likely to enhance Botha's image as an anticommunist strongman.