A judiciary source, who declined to be named, confirmed comments by Judiciary spokesman Ghulam Husayn Ilham to the ISNA students news agency earlier on Tuesday that the Supreme Court had scrapped Aghajari's death sentence.
"Yes, the sentence has been revoked," the source said.
Reformist history lecturer Aghajari was convicted by a provincial court of blasphemy in late 2002 for saying in a speech Muslims were not "monkeys" to blindly follow the teachings of senior clerics, comments deemed as a challenge to Iran's clerical establishment.
Aghajari's case was seen by political analysts as a litmus test of the limits of free speech in the Islamic Republic.
The sentence sparked the biggest pro-democracy protests in years and has been roundly criticised by senior clerics who said it was excessive and invited international criticism.
Aghajari's lawyer Salih Nikbakht said he had received no official word of the Supreme Court's decision.
He said Aghajari was likely to remain in jail for other convictions, including spreading lies and inciting public opinion - charges that stemmed from the speech he made in the western province of Hamadan two years ago.
"He is not going to be released immediately because of his other charges," Nikbakht said.
As well as being sentenced to death, Aghajari's original conviction included an eight year jail term, a 10-year teaching ban and banishment to remote desert cities for several years.
"He is not going to be released immediately because of his other charges"
Such multiple sentences are common in Iran.
Supreme Leader Ayat Allah Ali Khamenei, the top figure in Iran's clerical establishment, has twice intervened and called for a review of Aghajari's death sentence.
His latest intervention came last month after a court in Hamadan upheld the death sentence after Aghajari's lawyer appealed.
Khamenei's comments and stern criticism of the sentence by hardline commentators and senior clerics led most legal experts in Iran to deduce Aghajari's death sentence would eventually be scrapped and replaced with a jail term.