Saudi shut its side of Qatar’s only land border in June 2017 as part of a package of sanctions it said was a response to Doha’s backing radical Islamist groups and closeness to Iran.
Qatar always denied the charges.
AFP correspondents saw cars making the crossing on Saturday. A Qatari source said traffic at the Abu Samrah crossing, 120 kilometres (75 miles) south of Doha, had resumed around 0700 GMT.
Saudi Arabia, along with the United Arab Emirates, Bahrain and Egypt, all of which also imposed embargoes on travel and trade, had agreed to lift the restrictions at a Gulf Cooperation Council summit in the kingdom on Tuesday.
The day before the summit, Kuwaiti Foreign Minister Ahmad Nasser Al-Sabah had announced on state television that a deal had been reached to “open the airspace and land and sea borders between the Kingdom of Saudi Arabia and the State of Qatar”.
Qatar Airways and Saudi Airlines announced Saturday on Twitter that they would begin resuming flights between their countries from Monday.
Only a trickle of cars arrived at the palm tree-lined, whitewashed land border post to make the short crossing into Saudi Arabia after news broke that the frontier had reopened.
A smaller number made the journey from the kingdom into Qatar, where strict measures to fight the spread of the novel coronavirus have been imposed.
“I’m very happy the border is open again,” said Qatari Jaber al-Marri, as he approached a checkpoint in his Land Cruiser SUV, adding that he had loved ones in the neighbouring kingdom.
“A lot of Qataris have relatives in Saudi Arabia,” he said, holding a negative coronavirus test report.
“The coming days will be better.”
Qatar has announced strict coronavirus control measures for those arriving from Saudi Arabia.
Doha will require travellers to present a negative coronavirus test, undergo another test at the frontier and quarantine in a government-approved hotel for one week.
A helicopter belonging to the Qatari health service shuttled supplies between Doha and the border, an AFP correspondent reported.
As it was the weekend, cargo haulage did not appear to have resumed.
Qatari Hamad al-Marri, who also drove a Land Cruiser, said he was excited to go hunting with falcons in Saudi Arabia, a popular Gulf pastime.
“I’ll take a fortnight holiday there,” he said. “I will go hunting and visit my friends, whom we have not seen for more than three and a half years.”
“I’ll be reunited with my family,” he added. “Everybody is happy that we can go to Mecca and Medina.”
The two Saudi cities are focal points of Islam, but Qataris had struggled to undertake the Hajj and Umrah pilgrimages during the diplomatic rift.
Qatar and Saudi Arabia blamed each other for the hurdles.
Several drivers gathered at a petrol station close to the Qatari exit point just hours after the Kuwaiti announcement of a detente between Qatar and its erstwhile rivals.
“It’s a great joy, I bought this new car, a Land Cruiser, in order to go and celebrate with my relatives in Saudi Arabia,” said Zaid Muhammad al-Marri, 23, a Qatari with a Saudi mother.