"Abdullah Alsaidi has submitted his resignation to protest at the use of violence against demonstrators," a Yemeni foreign ministry official said on Sunday.
The move comes as Yemen's most powerful tribal confederation called on Saleh to step down.
Sheikh Sadiq al-Ahmar, the leader of Hashed, which includes Saleh's tribe, issued a statement asking the president to respond to the people's demands and leave peacefully. It was co-signed by several religious leaders.
Thousands were joining Sunday's burial procession of some of the 52 protesters killed on Friday, the bloodiest single day of the month-long uprising.
Around 30 bodies were laid out in neat rows and the square near Sanaa University overflowed with mourners, who massed under tight security and despite a two-day-old state of emergency.
Saleh had declared Sunday a national day of mourning for the "martyrs for democracy," while blaming the opposition for "incitement and chaos" that had led to the killings.
The violence prompted condemnation from the UN and the US, which backs his government with hundreds of millions in military aid to battle an al-Qaeda offshoot based in Yemen's mountainous region.
Police on Saturday stormed a protest camp in the southern port city of Aden and fired tear gas and live rounds, wounding three anti-government demonstrators.
Ministerial resignations
The escalation of violence has rocked the government of Saleh, and resulted in several ministerial resignations.
Muslim clerics called on Yemeni soldiers to disobey orders to shoot at demonstrators, and blamed Saleh for the slaughter on Friday.
"We call on the army and security forces to not carry out any order from anyone to kill and repress" demonstrators, a group of influential clerics said in a joint statement.
"The defections are on all sides and this is just the beginning," Abdul Ghani Al Iryani, a political analyst in the capital, Sanaa, told Al Jazeera.I think if we don't come to some kind of national reconciliation, the defections will continue until the regime falls.
"The president is talking to various political groups but he's not talking to the main group, which is the youth in the square.
"If he wants to get out of this, he will have to address their concerns, he'll have to include them in any national dialogue and he will have to accept the fact that much of his power needs to be transferred to a government of national unity."
Twenty-four parliamentarians have resigned from the ruling party.
Huda al-Baan, Yemen's human-rights minister, said she had resigned from the government and the ruling party in protest over the sniper attack on demonstrators.
Al-Baan said in a statement late on Saturday that her resignation was to protest the "massacre" of demonstrators demanding the departure of Saleh, who has been in power since 1978.
The undersecretary at the ministry, Ali Taysir, also resigned.
Al-Baan became the third Yemeni minister to resign over the past few weeks.
Nabil al-Faqih, the minister of tourism, resigned on Friday over the "unjustifiable use of force" against protesters, while the minister of religious endowments Hamoud al-Hattar resigned earlier in the week.
The chief of the state news agency has also stepped down, along with Yemen's ambassador to Lebanon.
Witnesses said pro-government "thugs" on Friday rained bullets from rooftops near a square close to Sanaa University, which for weeks has been the centre of demonstrations calling for the end of Saleh's rule.
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