"My deep condolences... We worked very closely," tweeted Araqchi, who took part in the negotiations for a hard-won nuclear deal agreed between Iran and world powers in 2015, AFP reported.
"I commend his skillful and professional performance... (that) resulted in complete closure" of the file on the "possible military dimension" of Iran's nuclear program.
"May the Almighty bless his soul," he wrote in English.
Amano died after suffering poor health for some time, the atomic agency said.
The longtime Japanese diplomat, who was 72, had held the IAEA's top job since December 2009.
During his tenure, Amano oversaw the signing of the landmark deal between Iran and six major powers – Britain, China, France, Germany, Russia and the US.
Under the deal, the Islamic Republic agreed to curb its nuclear program in exchange for the lifting of the sanctions.
In December 2015, the IAEA said it "has no credible indications of activities in Iran relevant to the development of a nuclear explosive device."
In his tweet, Araqchi noted that under Amano the IAEA had issued "15 consecutive reports confirming Iran's full compliance" with the nuclear accord.