A South Korean court on Monday acquitted Lee Jae-yong, Samsung’s top executive, on charges of stock price manipulation and accounting fraud, the latest twist in the billionaire’s legal troubles tied to a merger that helped him secure control of the nation’s largest company.

A Seoul district court judge said that there was not enough evidence to prove the prosecutors’ charges against Mr. Lee and 13 other current and former Samsung officials, including the accusation that the primary intent of the merger was to strengthen Mr. Lee’s power over the conglomerate, against the business interests of each Samsung affiliate that merged.

Prosecutors had sought a prison sentence of five years and a fine of 500 million won against Mr. Lee, 55. He has denied any wrongdoing. Prosecutors have the option to appeal the decision to a higher court. Neither Samsung Electronics nor the prosecutors’ office immediately commented after the verdict.

Mr. Lee’s lawyers said in a statement that the decision “clearly confirmed the legality” of the merger and the accounting of its affiliates.

Samsung is the largest and most successful of the South Korean conglomerates known as chaebol. The group’s electronics arm, Samsung Electronics, alone accounts for about one-sixth of the country’s exports. Mr. Lee, also known as Jay Y. Lee, is South Korea’s wealthiest individual according to Bloomberg News, which estimated his net worth at about $9 billion.

Some South Koreans speak proudly of the chaebol for having helped transform the country from a war-ravaged agrarian economy into a global export powerhouse. But others have increasingly scrutinized whether they stifle smaller businesses or make corrupt deals with government officials without facing enough repercussions.

Most chaebol scandals have stemmed from the families’ attempts to ensure that the next generation inherits control, such as arranging for scions to buy shares of subsidiaries at discounted prices.

Business experts in South Korea said that they were surprised by Monday’s verdict, which they said raised concerns about the fairness of the country’s markets and the credibility of its judiciary.

“This case confirms a judicial system that is more backward than it was in the past,” said Sung-In Jun, an economics professor at Hongik University in Seoul, “and how powerless the South Korean political and judicial authorities are in front of the chaebol.”

Mr. Lee’s legal troubles began when massive protests in Seoul led to the 2016 impeachment of former President Park Geun-hye on charges of collecting or seeking bribes from Samsung and other chaebol and for abusing her power. Ms. Park was jailed in 2017 and pardoned and released in 2022.

Mr. Lee was arrested in 2017 on charges of bribing Ms. Park and her confidante, Choi Soon-sil, to win the government’s support for a 2015 merger of two Samsung subsidiaries at the center of the corruption scandal. He was the vice chairman of Samsung Electronics at the time.

Prosecutors had said the merger was a step in Mr. Lee’s effort to transfer the control of Samsung from his father, Lee Kun-hee, who was incapacitated by a heart attack in 2014 and had been twice convicted and pardoned of bribery and tax evasion years before. A New York-based hedge fund, Elliott Management, launched a campaign urging shareholders to vote against the merger. But the country’s National Pension Service, which was a major shareholder of one of the subsidiaries, voted in favor of the merger in return for Mr. Lee’s bribes, prosecutors said.

A Seoul district court in 2017 sentenced Mr. Lee to five years in prison for offering 8.9 billion won in bribes to Ms. Park and to Ms. Choi.

His case wound its way through the court system over the next two years, with Seoul’s High Court reducing his sentence and releasing him from prison in 2018. The nation’s Supreme Court ordered a retrial in 2019.

While he waited for the retrial in 2020, Mr. Lee was indicted on a charge of stock price manipulation and accounting fraud, the case whose verdict was announced on Monday. But prosecutors were unable to arrest him because a court had refused to issue an arrest warrant.

The prosecutors had accused Mr. Lee and other current and former Samsung officials of committing those crimes in the 2015 merger. His lawyers said the merger had taken place in accordance with the law.

During the retrial on the bribery charges in 2021, the Seoul High Court sentenced Mr. Lee to two and a half years in prison, finding the bribes had totaled 8.6 billion won.

Later that year, the Justice Ministry released him on parole, along with 800 other prisoners, on a holiday commemorating the end of Japan’s colonial rule over Korea at the end of World War II. South Korea often paroles or pardons prisoners on important national holidays.

Business analysts were split on whether Mr. Lee’s time in prison had an impact on his empire. Samsung Electronics became the world’s most profitable technology company while he was in prison. Others said Samsung was postponing key decisions with Mr. Lee in jail and fell behind competitors like TSMC.

At the time of his release in 2021, he was still banned from employment at Samsung for five years. That was lifted in 2022 when he won a pardon from President Yoon Suk Yeol, who as a prosecutor had led the investigation of Mr. Lee.

Two months later, Samsung Electronics named Mr. Lee executive chairman, elevating him less than 15 months after he was released from prison for bribery.