How this development will pan for Iran's new government and if could presage escalation to a much wider conflict in the volatile region beyond Gaza and the Israel-Lebanon border remains to be seen, but the initial effect will be on the off-and-on negotiations for a halt to fighting in Gaza and the release of the remaining hostages.
Details of the assassination incident are still sketchy but according to the Islamic Revolutionary Guard Corps, a residence for war veterans in north Tehran where the Hamas leader was living was hit by a projectile at around 2 a.m., killing him and one of his bodyguards. There have not been any claims of responsibility, but Iran and the Hamas have blamed Israel.
The development is awkward for Iran, as the incident came hours after representatives from 88 countries were in the country for Pezeshkian's inauguration and its response was unequivocal and strident.
Supreme Leader Ayatollah Seyyed Ali Khamenei said that by assassinating Haniyeh, the Israeli regime has "prepared the ground for harsh punishment for itself", as per Iranian media reports.
Iran considers its duty to take revenge for the assassination of Haniyeh who was martyred in the territory of the Islamic Republic of Iran, he added.
Pezeshkian's reaction was no less strong, as he stressed that the country would defend its "territorial integrity and dignity".
"...Yesterday I raised his victorious hand and today I have to carry his coffin on my shoulders", he said in a post on X.
"The bond between the two proud nations of Iran and Palestine will be stronger than before, and the path of resistance and defence of the oppressed will be followed stronger than ever", he said, adding that Iran "will defend its territorial integrity and honour and would make the terrorist occupiers regret their cowardly action".
The IRGC, in a statement, warned "the Zionist regime" of a "harsh and painful response" for the assassination.
Meanwhile, the National Security and Foreign Policy Committee of the Iranian Parliament was slated to hold an emergency meeting on Wednesday itself over the assassination.
"The issue is under investigation and the National Security and Foreign Policy Committee will announce the necessary information regarding the next actions and meetings," Committee spokesman Ebrahim Rezaei told reporters, IRNA reported.
The targeting of Haniyeh comes shortly after Israel attacked Beirut to eliminate a top Hezbollah leader and claimed success, though local authorities did not confirm the fate of Fuad Shukr.
As noted Qatar, which was leading the negotiation efforts along with Egypt, has reacted strongly to the assassination of Haniyeh, who used to live in exile in the country.
Its Foreign Ministry termed it "a heinous crime, a dangerous escalation, and a flagrant violation of international and humanitarian law", underlining that "the assassination and reckless targeting of civilians will lead the region into chaos and undermine the chances of peace".
Qatar's PM and Foreign Minister Mohammed bin Abdulrahman bin Jassim Al Thani was more blunt. "Political assassinations & continued targeting of civilians in Gaza while talks continue leads us to ask, how can mediation succeed when one party assassinates the negotiator on the other side? Peace needs serious partners & a global stance against the disregard for human life," he said in a post on X.
On the other hand, the targeting of Haniyeh, one of the most prominent Hamas leaders along with Khaled Meshal - the target of a bungled Israeli assassination plot decades back - and Mahmoud Zahar, makes for good optics for the supposed beneficiary but is scarcely a strategic advantage.
Considered a pragmatist, if not moderate, and open to political solutions, Haniyeh's removal from the scene could mean the leadership mantle switch back to shadowy - and more unrestrained - figures like Yahya Sinwar, perceived as the mastermind of the October 7, 2023 attacks.
The long-term implications could be similar for Israel - and the West at large, after the 1967 Arab-Israeli War, when secular nationalist rulers like Egypt's charismatic Gamal Abdel Nasser were humbled, and the stage set for Islamist fundamentalists to come to the fore. Israel repeated the same mistake in the 1970s when it backed the incipient Hamas to undermine Yasser Arafat and the left-leaning and secular PLO, and in the process, ended up creating a bigger problem for itself.
The actions of the principal actors in days to come will determine if the Tehran assassination remains a one-off incident or a trigger to more instability, and suffering.