Earlier, leaders including the emirs of Kuwait and Qatar, the king of Bahrain and the UAE vice president arrived in Saudi Arabia for a previously unannounced summit aimed at resolving their differences.
Local media reported last week that leaders of the six-nation alliance, which also includes Oman, were expected to hold a meeting ahead of their annual summit in Doha on December 9-10, in a last-ditch bid to overcome internal differences.
Kuwait's emir Sheikh Sabah al-Ahmed al-Sabah has been leading a mediation effort to bridge the gap between Qatar and Saudi Arabia, the United Arab Emirates and Bahrain.
Qatar is accused of supporting the Muslim Brotherhood and offering a safe haven to other banned Islamist groups.
Saudi Arabia, the UAE and Bahrain all withdrew their ambassadors to Doha in March, sparking one of the Gulf Cooperation Council's worst diplomatic rows since its creation in 1981.
A GCC statement on Sunday said the agreement for the ambassadors to return to Doha "promises the opening of a new page that will present a strong base, especially in light of the sensitive circumstances the region is undergoing".
It said these circumstances "require extra effort" to safeguard the Gulf's security.
"Based on this, Saudi Arabia, the UAE and Bahrain have decided to return their ambassadors to Doha," it said.
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The dispute had led to reports of the venue for the annual GCC summit being moved from Doha, although Kuwait last week denied any change.
A GCC foreign ministers' meeting which had been scheduled on November 10 to prepare for the summit was postponed as mediation efforts continued.
Saudi Arabia, Bahrain and the UAE had accused Qatar of meddling in their internal affairs by supporting the Brotherhood.
Riyadh and Abu Dhabi label the Brotherhood a "terrorist" group, and the UAE has jailed dozens convicted of links to the Islamist organisation.
Doha earlier this year asked Brotherhood leaders to leave Qatar following diplomatic pressure from Saudi Arabia.
The UAE on Saturday issued a list of 83 Islamist groups which it classified as "terrorist organisations", among them the Qatar-based International Union of Muslim Scholars, which is headed by the Brotherhood's spiritual guide Sheikh Yusuf al-Qaradawi, a Qatari citizen.
In August, Oman's Foreign Minister Yussef bin Alawi bin Abdullah and the Kuwaiti emir said after a GCC meeting in the Saudi city of Jeddah that the dispute with Qatar had been resolved and the ambassadors would return to their posts in Doha.
But no date was given for the envoys' return, and differences remained.
The following month Saudi Arabia and Qatar, along with Bahrain and the United Arab Emirates, joined a US-led coalition against extremists of the Islamic State group in Syria.
Advances by the jihadists in Syria and Iraq, and US calls for a coalition against them, helped pull the Gulf monarchies closer, analysts said.