JERUSALEM, SEPT. 2 -- Moshe Arens, a main architect of the Lavi jet fighter project, tonight submitted his resignation from Israel's Cabinet to protest its decision to scrap the aircraft. His move is a political blow to Prime Minister Yitzhak Shamir, who counted Arens his closest ally in the Cabinet.

Shamir is expected to seek vigorously to persuade Arens to change his mind during the next 48 hours, after which the resignation becomes effective.

If he fails, Shamir will lose not only his firmest supporter in the 10-member inner cabinet, the ultimate arbiter of policy decisions in Israel's fractious coalition government, but also the man he is believed to favor in future succession wars inside his own political party.

Arens' resignation follows Sunday's Cabinet meeting, at which ministers voted 12 to 11 to cancel the troubled project, which some experts predicted would run as much as $2 billion over its budgeted costs during the next decade.

The vote was largely along party lines, with the Likud bloc of Shamir and Arens voting for the plane, while Foreign Minister Shimon Peres and his Labor Alignment voted against it.

The Reagan administration, which has provided most of the $1.5 billion spent so far on the project, had strongly urged the Cabinet to cancel it, as had Israel's military command, arguing it would consume funds needed for other weapons systems.

Speaking to reporters tonight, Arens acknowledged that Shamir and others had sought to dissuade him from quitting, but he said, "The only thing that could have changed my mind is to revise this sorry decision. It has negative implications and hurts thousands of dedicated people."

Arens lashed out at Peres and the Labor Party, saying it had politicized the Lavi decision and "tricked" the Likud by enforcing party discipline on Health Minister Shoshana Arbelli-Almoslino, compelling her to abstain on the vote when she had previously pledged to support the project. By contrast, he noted, Likud Finance Minister Moshe Nissim was allowed by his party to vote his conscience and oppose the plane, the only Likud member who did so.

Arens' resignation followed a three-hour meeting of Likud ministers today in which they pledged to support another vote but took no steps to enforce party discipline on Nissim. Outside, 200 Lavi workers noisily demonstrated, blocking traffic until they were dispersed by police.

In contrast to Arens, most Likud ministers privately appeared satisfied with the outcome of Sunday's decision because their Labor opponents took the burden of killing a project that remains politically popular even though it had become a costly white elephant.

Shamir's aides have said the Likud intends to capitalize on the Lavi in next year's planned general elections. But the loss of Arens could negate some of that political advantage for the prime minister.

"Shamir is very sorry about this resignation," said a source close to the prime minister who insisted on anonymity. "He doesn't see it as a logical step and he thinks it's a shame. But it will hurt Arens more than anyone else. It's a fact of political life in Israel that anyone who resigns is quickly forgotten."

But other analysts said Arens' departure would harm Shamir's standing in both the party and the inner cabinet, where Shamir's Likud bloc controls five seats.