The Egyptian-born cleric, who has close links to the Muslim Brotherhood, has been critical of Egypt's military-installed government, accusing Sisi of betrayal for ousting the country's first freely-elected President Mohamed Morsi last year, Reuters reported on Sunday.
Qaradawi's outspoken support for the Brotherhood has recently contributed to an unprecedented diplomatic rift between Qatar and fellow Persian Gulf Arab kingdoms which view the Brotherhood as a security threat and therefore supported the coup against Morsi.
"People of Egypt in the capital and the provinces, cities and villages, sit in your houses and do not burden yourselves with a great sin...," Qaradawi said in an emailed statement.
"It is not permissible for you to vote for he who has disobeyed God," he added.
Sisi is expected to easily win the May 26-27 presidential election. His only challenger is leftist politician Hamdeen Sabahi, who came in third in the 2012 vote won by Morsi.
The Brotherhood maintains that Sisi staged the coup against Morsi and masterminded his removal.
"The duty of the nation is to resist the oppressors, restrain their hands and silence their tongues," said Qaradawi.
He further insisted that Sisi's victory in the poll would please the "Zionists," referring to Israel, and "enemies of the nation."
Persian Gulf Arab states have been unhappy with Doha for sheltering Qaradawi, a major critic of Saudi and UAE authorities, and for giving him air time on its pan-Arab satellite and state television channels.
Saudi Arabia, the UAE and Bahrain were especially angry over Qatar's support for the Muslim Brotherhood, whose ideology challenges the principle of despotic rule that dominates the region.
NTJ/MB