However in a critical Twitter thread, Israel's Lior Haiat said he is "an extremist figure, committed to Iran's rapidly advancing military nuclear program".
Iran and Israel have been in a long-running "shadow war", which has resulted in both countries taking part in tit-for-tat actions, but so far avoiding all-out conflict. Recently, however, the hostilities between the two have escalated again.
The situation is complex, but one big source of tension is Iran's nuclear activities.
Meanwhile, Israel does not believe that Iran's nuclear programme is purely peaceful, and is convinced it is working towards building a nuclear weapon.
The 2015 Iran nuclear deal, which saw harsh penalties lifted on Iran as long as it stopped some nuclear work, collapsed when former US President Donald Trump abandoned the deal in 2018, and re-imposed the crippling economic sanctions. The Biden administration is now trying to work out a way to re-enter the deal.
In response to the sanctions being tightened, Iran stepped up its nuclear activities, and is currently enriching uranium at its highest levels ever - although still short of what is needed to make nuclear-grade weapons.
1/4 After the Supreme Leader effectively dictated to the Iranian public who they could choose, less than 50% of Iranian citizens eligible to vote have elected its most extremist president to date. pic.twitter.com/gYuBdUNMqx
Commenting on the election result, the US said it regretted Iranians were "denied their right to choose their own leaders in a free and fair electoral process".
Voter turnout was at a record low for this election, with less than 50% of registered voters going to the polls, compared to more than 70% in 2017. Many people shunned the election, believing that it had been engineered in favour of Mr Raisi, who is a staunch ally of Supreme Leader Ayatollah Ali Khamenei.
Mr Raisi's win has come on the same weekend as negotiations to try and save the Iran nuclear deal continue in Vienna.
The EU has said another formal meeting will take place on Sunday between Iran and the six world powers involved in the deal. This is the sixth round of indirect talks between the US and Iran, and this week officials said the parties remain divided on some key issues, Reuters reported.
'The butcher of Tehran'
In his Twitter thread, Lior Haiat called Mr Raisi the "butcher of Tehran", in reference to the mass execution of thousands of political prisoners in 1988.
Mr Raisi was one of four judges, who became known as the "death committee", which allegedly sentenced about 5,000 men and women to death, Amnesty International says. In his tweets, however, Mr Haiat said more than 30,000 people were killed, which is a number also referenced by Iranian human rights groups.
What about the reaction from elsewhere?
Russia's Vladimir Putin was quick to congratulate Ebrahim Raisi, highlighting the "traditionally friendly and good-neighbourly" relationship between the two countries.
The leaders of Syria, Iraq, Turkey and the UAE sent similar messages of support and congratulations.
A spokesperson for Hamas, the Palestinian militant group that runs Gaza, wished Iran "progress and prosperity".
However, human rights groups have said Mr Raisi should be investigated for atrocities.
"As head of Iran's repressive judiciary, Raisi oversaw some of the most heinous crimes in Iran's recent history, which deserve investigation and accountability rather than election to high office," Michael Page from Human Rights Watch said.