Officials on Monday sought the arrest of Lee Jae-Yong on charges of bribery, embezzlement and perjury, sending shock waves through the group, which is a major part of the South Korean economy and includes the world's largest smartphone maker.
It is already reeling from the debacle over the recall of its flagship Galaxy Note 7 device and reports have suggested it could face sanctions from overseas authorities if Lee is punished.
But the court rejected the request on grounds of insufficient evidence, which could mar investigators' plan to question Park -- impeached by parliament last month -- on charges of bribery.
A spokesman for the prosecution team described the decision as "very regrettable" but said they will "carry on with our probe without wavering".
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Analysts questioned the decision.
Kim Nam-Geun, a Seoul lawyer and a political commentator, accused the court of being soft on Samsung because of media pressure and the potential wider economic impact of Lee's arrest.
Samsung is South Korea's largest business group and its revenue is equivalent to about a fifth of the country's GDP.
As well as the investigation of Park, the decision could weaken prosecutors' probes into the heads of other conglomerates implicated in the scandal, said Choi Chang-Ryol, a professor of politics at Yongin University.
"It would be far easier for prosecutors to quiz Lee if they have him under detention, and eventually build a bribery case against Park as well," he said.
With a slight smile, wearing a long coat and tie and carrying a shopping bag, he was led out by a security guard to a barrage of camera flashes, and was driven away without responding to questions from a horde of journalists.
Investigators said Lee gave or promised some 43 billion won (USD 36.3 million) worth of bribes to Choi, allegedly in return for the state pension fund's backing of a merger of two Samsung affiliates -- deemed crucial for Lee's hereditary succession at Samsung.
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