Ehud Olmert, a former prime minister of Israel, was acquitted of corruption charges in two matters by a Jerusalem court on Tuesday, but convicted in a third, in a high-profile corruption prosecution that cut short his term in office and changed the course of Israeli politics and diplomacy.

Mr. Olmert was convicted of breach of trust, the least serious of the charges he faced, and will be sentenced in September, according to court documents.

The result immediately raised questions about the motives and the zealousness of police investigators and state prosecutors in pursuing the case. It was also likely to raise the question of a possible political comeback for Mr. Olmert, who resigned as prime minister in 2008. But he is still embroiled in another serious corruption case, in which he is charged with taking bribes in connection with the construction of a huge residential complex while he was the mayor of Jerusalem.

Mr. Olmert’s three-year tenure as prime minister was marked by high-wire peace talks and military actions and dogged by multiple police investigations. Intensive talks with the Palestinians were interrupted by a devastating three-week Israeli offensive in Gaza in the winter of 2008-2009, and the elections that followed Mr. Olmert’s resignation brought Benjamin Netanyahu of the conservative Likud Party to power. The peace process has largely been stalled since then.

Mr. Olmert has acknowledged making mistakes in the years before he became prime minister, but has always denied criminal wrongdoing. His lawyers maintained that he would prove his innocence in court.

Quoting Menachem Begin, a predecessor as prime minister, Mr. Olmert declared on Tuesday, “There are judges in Jerusalem.”

Mr. Begin, a stickler for the law, uttered those words in the late 1970s in a very different context, after Israel’s Supreme Court accepted the state’s position allowing the expropriation of land for a Jewish settlement in the West Bank. For Israelis, the phrase has come to symbolize the principle that the law and the judicial system should always stand above the government.

Mr. Olmert came of age politically in Mr. Begin’s Likud Party, but by the time he became prime minister, he was the leader of Kadima, a centrist party established in 2005.

Mr. Olmert was visibly relieved at the verdict on Tuesday. Acknowledging that he had become a bit emotional, he said he respected the court’s decision regarding the breach-of-trust charge, on which he was convicted, and that he would “learn the necessary lessons.” Still, he insisted that the matter, known as the Investment Center affair, amounted to procedural irregularity rather than corruption. In that affair, which took place when he was minister of trade and industry, Mr. Olmert was charged with making decisions that benefited clients of a close associate.

Mr. Olmert has kept a relatively low profile for most of the years since he left office, but on Tuesday he promised that Israelis would be hearing much more from him.

Eli Zohar, the attorney who led Mr. Olmert’s defense team, said the verdict made Tuesday “a great day, first of all, for Israeli justice.”

Eli Abarbanel, a Jerusalem district attorney, said that while the result was unexpected, “we cannot dismiss the fact that such a senior figure was found guilty — the court strongly criticized his conduct.”

Ram Caspi, a prominent Israeli lawyer, told Israel’s Channel 2 television that he saw Tuesday as a “sad day for Israel” because a prime minister had been pushed out of office, only to be cleared at trial.

The panel of three judges ruled unanimously that the evidence did not prove beyond doubt that Mr. Olmert had acted with criminal intent in the most sensational of the three matters at trial, which involved Morris Talansky, an American businessman whose testimony was instrumental in Mr. Olmert’s downfall. Israelis were stunned in May 2008 when Mr. Talansky told a court here that he had given about $150,000 to Mr. Olmert over 13 years, mostly in cash stuffed into envelopes, a claim Mr. Olmert denied.

Mr. Talansky said at the time that much of the money was earmarked for election campaigns, but that some was for Mr. Olmert’s personal expenses. It included at least $25,000 meant for a vacation in Italy and almost $5,000 to cover Mr. Olmert’s bill at a Washington hotel because Mr. Olmert’s own credit card was “maxed out,” Mr. Talansky testified, adding that some of the money was intended as a loan but was never repaid.

According to the prosecution, the money was provided between 1992, when Mr. Olmert first ran for mayor of Jerusalem, and late 2005, when Mr. Olmert was minister of industry and trade. He became prime minister in early 2006.

Mr. Olmert declared outside the court on Tuesday that “there were no envelopes of money and there are no envelopes of money.” He added, “It never happened.”

The second matter in which Mr. Olmert was cleared involved accusations that, while mayor of Jerusalem and later while in the cabinet, he billed multiple state and charitable agencies for the same travel expenses and used the extra money for private family trips. He was indicted in that case in August 2009.