The 48-year-old Lee, scion of the country's richest family, was taken into custody at the Seoul Detention Centre after waiting there overnight for the decision. He was being held in a single cell with a TV and desk, a jail official said.
Lee is a suspect in the influence-peddling scandal that led parliament to impeach President Park Geun-hye in December, a decision that if upheld by the Constitutional Court would make her the country's first democratically elected leader forced from office.
Shares in flagship Samsung Electronics Co Ltd fell 1.1 percent, while shares in Samsung Camp;T Corp, the de facto holding company of Samsung Group, were down 2.8 percent compared with the wider market's .KS11 drop of 0.2 percent.
Prosecutors have up to 10 days to indict Lee, Samsung's third-generation leader, although they can seek an extension. After indictment, a court would be required to make a ruling within three months.
No decision had been made on whether Lee's arrest would be contested or whether bail would be sought, a spokeswoman for Samsung Group said.
Samsung and Lee have denied wrongdoing in the case.
"We will do our best to ensure that the truth is revealed in future court proceedings," the Samsung Group said in a brief statement after Lee's arrest.
The same court had rejected a request last month to arrest Lee, but prosecutors on Tuesday brought additional accusations against Lee, seeking his arrest on bribery and other charges.
"We acknowledge the cause and necessity of the arrest," a judge said in his ruling.
The judge rejected the prosecution's request to arrest Samsung Electronics president Park Sang-jin.