A military disciplinary board acquitted the Israeli Army's chief infantry and paratroop officer today of charges of "violent behavior" and conduct unbecoming an officer in the pistol-whipping of two Arab hijackers who died last year after they were led handcuffed from a bus in the Gaza Strip to be interrogated.

The board ruled that the injuries caused by Maj. Gen. Yitzhak Mordecai with the butt of his pistol were "not unreasonable" in light of the circumstances surrounding the interrogation of the Arabs, both of whom died shortly afterward of skull fractures. The board's chairman, Maj. Gen. Haim Nadel, ruled that the interrogation was carried out "in order to obtain vital and immediate information" in time to prevent injuries from a suspected bomb left on the hijacked bus.

The board rejected recommendations by Israel's attorney general and a special inquiry commission that Mordecai be prosecuted for causing grievous bodily harm to the two hijackers while they were in custody.

"The injury done by Mordecai to the terrorists and the incident under discussion is not unreasonable in light of the endangerment to human lives he sought to prevent," Nadel declared in acquitting Mordecai of all charges.

Mordecai has not denied beating the two hijackers with his pistol butt in the April 1984 attack, but he has maintained that in order to pre-vent a further loss of lives it was essential to determine whether a live bomb had been planted on the bus.

The investigating commission said last week that the two hijackers were taken off the bus to a field where they were beaten with a blunt instrument while being interrogated. It said it had "turned up prima facie evidence regarding use of violence toward the two terrorists, via blows with a pistol, by [then-] Brig. Gen. Yitzhak Mordecai."

That panel said that because it was impossible to establish from medical evidence whether the hijackers died from the blows delivered by Mordecai or from injuries sustained during the storming of the bus by security forces, Mordecai could not be held directly responsible for the deaths.

It concluded, however, that Mordecai had committed grievous bodily harm to the two Arabs, and suggested that he should be tried on that charge and on a charge of conduct unbecoming an officer.

It also recommended prosecution of five members of the Shin Bet secret security force, three policemen and three other soldiers implicated in the beatings. Observers said today that it now appeared unlikely that those members of the security forces, subordinate to Mordecai, would be prosecuted.

A soldier was killed and eight other bus passengers were injured when a commando force stormed the bus, which had been hijacked by four Palestinian terrorists on the coastal road in Israel and driven to Gaza. Two hijackers died during the assault on the vehicle.

Attorney General Yitzhak Zamir, concurring with the inquiry panel's findings last week, had cited a May 1984 statement by Defense Minister Yitzhak Rabin condemning "the behavior that led to the deaths of the two terrorists captured on the bus, behavior that clearly contradicts basic regulations and norms." Rabin added, "Not even the special circumstances of the situation justify such behavior."

After recommending that Mordecai be prosecuted, Zamir came under intense criticism from right-wing members of parliament, some of whom urged that he be fired.

Mordecai's supporters argued that the general was acting under "battlefield conditions" when he interrogated the two hijackers, and should not have been held to standards of conduct that apply during peacetime.