It ruled that there was insufficient reason to arrest him.
He was later seen leaving the Seoul detention centre where he had been awaiting the ruling.
The allegations were part of a corruption scandal which led parliament to impeach President Park Geun-hye.
Mr Lee had been waiting for the ruling for more than 12 hours, since a hearing on Wednesday.
"The merits of this case can now be determined without the need for detention," Samsung said in response to the court order.
A spokesman for the court said the long wait for the ruling was because the judge had needed time to consider various factors before making a decision.
South Korea's special prosecutors made a formal request for an arrest warrantearlier this week.
Correspondents say their hopes of stretching criminal proceedings to include the president - who was stripped of her powers last month - may have been knocked off course by the refusal to issue a warrant against Mr Lee.
Samsung has consistently denied any wrongdoing.
The electronics giant is accused of giving donations to non-profit foundations operated by Choi Soon-sil, a friend of Ms Park, in exchange for government favours.
It has admitted making payments but insists it did not expect any favours in return.
Mr Lee, also known as Jay Y Lee, gave evidence at Seoul Central District Court on Wednesday.