The bench, however, said the warrant against Lee would not be executed for six weeks.
Lee faced the warrant after he did not appear in the case before the trial court where the supplier has lodged a cheating case against him.
JCE Consultancy had filed a complaint against Lee in the Ghaziabad court alleging Lee had cheated him of $1.4 million.
Lee is South Korea's richest man with a net worth of $11.2 billion, according to Forbes.
In a statement, Samsung said Lee had no connection with the case, which it said was related to a "multi-million dollar fraud scheme" perpetrated against a subsidiary in Dubai.
"There are no grounds, let alone evidence, to support the accusation against Chairman Lee," the company said. "We are confident that the Indian courts will recognise the innocence of Chairman Lee and deliver justice."