In a televised appearance on the Hezbollah-owned Al Manar TV, Hassan Nasrallah said on Sunday that Hariri's resignation speech was "written by Saudi".
"It was not our wish for Hariri to resign," he said of the sudden and unexpected move.
"Even if he was forced to resign, the way in which it was executed does not reflect Hariri's way in dealing with things," Nasrallah added, questioning the text of Hariri's speech broadcast during his visit to the Saudi capital, Riyadh, on Saturday.
Hariri said Iran fomented "disorder and destruction" in the country and meddled in the internal affairs of Lebanon and other Arab states. He described Hezbollah as "Iran's arm" in the country.
"They have built a state within a state," said Hariri.
His resignation has stoked fears of an escalation in the regional divide between Iran and the Gulf states, primarily Saudi Arabia, with Lebanon on the front lines.
"It would have been better to allow him to go back to Lebanon, meet the president, submit his resignation, and declare it from the palace," said Nasrallah.
"The way in which it was delivered makes it clear that Saudi Arabia meddles in Lebanon's internal affairs ... The tone was not at all suitable. We need to discuss the Saudi element."
He also demanded to know the "real reason" behind the move, which he said Hariri owed to the Lebanese people.
Nasrallah questioned the motive behind the surprise resignation, suggesting possibilities such as Saudi internal conflicts.
"Is it a conflict relating to financial matters? A struggle between princes? Is Saudi not happy with Hariri's performance? Do they [Saudi officials] think he can be replaced by someone who would abide by Saudi policies?" he asked.
"Or maybe it has to do with Hezbollah - this is another possible reason."
He reassured the people of Lebanon of Hezbollah's commitment to maintain the country's "safety and stability".
Nasrallah concluded his remarks by saying Hezbollah will never be "pressured".
Al Jazeera's senior analyst Marwan Bishara said the speech was Nasrallah's attempt to contain and prevent further escalation.
"Saudi Arabia wants to escalate its proxy war with Iran - not only in Yemen and Syria, but also in Iraq and Lebanon," said Bishara.
"We're seeing now Lebanon being put in the middle of this proxy conflict between Iran and Saudi Arabia - with the Iranians really pushing hard in order to take more control of Lebanon through Hezbollah, as well as Saudi Arabia trying to expand its influence and confront Iran in places like Lebanon."
Hariri, a leading Sunni politician, had been in office for less than a year, but previously served as prime minister between 2009-2011.
He assumed office again in late 2016 in a power-sharing government headed by President Michel Aoun, a supporter of Hezbollah. Hariri's resignation now casts doubt on Lebanon's political future.