Seoul Central District Court judge Park Beom-seok, who reviewed the arrest warrant, said there was a risk of "destruction of evidence considering the gravity of the crime and circumstances revealed during the investigation" that justify Lee's confinement.
In January, Lee denounced the corruption investigation against him as a political maneuver aimed at destroying the country's conservatives, directing his criticism at the government of current President Moon Jae-in.
In the statement written the previous day, he said that the country faced a global financial crisis during his term, but successfully overcame it in the most exemplary way.
Lee, 76, who was president from 2008 to early 2013, has been the focus of a prosecution probe for five months. His successor Park is also behind bars for corruption and power abuse allegations, facing a prison sentence that could extend up to 30 years.
Lee is the fourth South Korean president to be arrested.
"Right now, I feel it's all my fault and I have a guilty conscience rather than blaming others", Lee said in a statement issued shortly before his arrest, according to Yonhap news agency.
Former President Lee Myung-bak is driven to a detention center on Thursday at midnight.
"Late President Roh Moo-hyun was also investigated for alleged corruption involving his family in 2009 while Lee was in office". She was dismissed by the Constitutional Court 21 days earlier.
Lee posted a message in his social media account after the arrest decision, saying he is responsible for everything though he tried his best during his presidency.
Lee's immediate successor, Park Geun Hye, was also removed from office previous year after being impeached and is now standing trial on charges of bribery, abuse of power and coercion.
In exchange for the payment, Samsung Electronics Chairman Lee Kun-hee is believed to have bought a presidential pardon in 2009 when the Samsung chairman, now in hospital, got a suspended jail sentence for tax evasion.
Prosecutors say Lee is the ultimate proprietor of the DAS fund.
The main opposition Liberty Korea Party Chairman Hong Joon-pyo, for his part, again accused the Moon administration of political revenge. Kweon Seong-dong, Kim Young-woo and Chang Je-won, gathered at his home around 8 p.m. Thursday, just a few hours before the detention warrant was issued.