Prince Khaled al-Faisal was speaking at a news conference to discuss the annual hajj pilgrimage, which ends on Thursday and has added to tensions between Riyadh and Tehran.
"I call on Muslim leaders, whether they are political leaders, ulemas (scholars), or intellectuals, to combat sectarianism," Faisal said.
For the first time in nearly three decades, Iran's 64,000 pilgrims are not attending the hajj in Sunni-dominated Saudi Arabia after the two regional rivals failed to agree on security and logistics.
"Combat this sectarian divide between Muslims. Islam is one and only one religion," Faisal said in Mina, a pilgrimage site on the edge of Makkah.
He said this year's hajj occurred without incident despite "the lies and allegations... of those who wanted to place in doubt the capacity of the kingdom to serve the pilgrims."
Among its concerns over Iranian participation in this year's hajj, Riyadh said Tehran had demanded the right to organise demonstrations.
Tehran in turn accused Riyadh of "blocking the path leading to Allah".
Security was one of the contentious issues following last year's hajj stampede which, according to foreign officials, killed roughly 2,300 people.
Iran reported the largest number of victims, at 464.
Just days before the hajj began on Saturday Iran's supreme leader Ayatollah Ali Khamenei questioned Saudi Arabia's right to manage Islam's holiest sites.
Saudi Arabia's Grand Mufti Abdulaziz al-Sheikh retaliated by telling a newspaper that Iranians "are not Muslims".
Reiterating a point made on Tuesday by King Salman, Faisal said Saudi Arabia does not interfere in Iran's internal affairs "but we don't permit the holy sites and the hajj to be used for political ends".
More than 1.8 million faithful from around the world have been attending the annual pilgrimage.
,I call on Muslim leaders, whether they are political leaders, ulemas (scholars), or intellectuals, to combat sectarianism,, Prince Khaled al-Faisal
The governor of Saudi Arabia's Makkah region on Wednesday urged Muslim religious leaders to fight sectarianism, an indirect criticism of Shia Iran.
