Foreign Minister Zarif responded to the remarks by reminding Trump that questions continue to swirl about the role that members of the Saudi monarchy played in the 2001 attacks.
Fifteen of the 19 hijackers affiliated with al-Qaeda who murdered nearly 3,000 people in New York in 2001 were citizens of Saudi Arabia.
In March, families of 850 victims who died on 9/11 and 1,500 people injured that day filed a lawsuit against the Saudi government, alleging that it provided material and financial support to the terrorist organization for years leading up to the tragedy.
"[Trump] must enter into dialogue with them about ways to prevent terrorists and takfiris from continuing to fuel the fire in the region and repeating the likes of the September 11 incident by their sponsors in Western countries," Zarif wrote in an opinion piece published by the London-based al-Araby al-Jadeed media outlet.
Zarif pointed out that while campaigning ahead of the US election, Trump himself suggested that the kingdom could be behind the attack.
"Who blew up the World Trade Center? It wasn't the Iraqis" Trump told Fox & Friends last February, "It was Saudi — take a look at Saudi Arabia, open the documents."
On Saturday, Washington and Riyadh signed a massive arms deal that could total up to $350 billion, one of the biggest single arms deals in US history.
In his article, Zarif also reacted to Saudi Deputy Crown Prince and Defense Minister Mohammed bin Salman saying that the kingdom "will work to have the battle in Iran rather than in Saudi Arabia" by offering peace to Saudi Arabia as a gift.
"The realization of this issue, however, depends on the Saudi government ending its futile war and deadly attacks against the Yemeni people and abandoning its crackdown on the pro-democracy majority in neighboring countries," he wrote.
Zarif pledged that Iran is committed to combating terrorism and restoring stability in the region.
"Today, the stable Iran is seeking stability in the entire region because it knows that achieving security at home at the expense of insecurity among neighbors is basically impossible," he said.