Passenger ships Wuzhishan, Tongguling, Zijing 12, and Baishiling collected a total of 3,553 Chinese nationals and were headed home, China's official news agency Xinhua reported.
The vessels, each with a capacity of about 1,000 people, had left the central Vietnamese port of Vung Ang and were en route to the southern Chinese port city of Haikou, Xinhua added.
Relations between the communist neighbours have plummeted following Beijing's move earlier this month to send a deep-water drilling rig into contested waters in the South China Sea.
Two Chinese nationals were killed and about 140 injured when enraged mobs torched or otherwise damaged hundreds of foreign-owned businesses in Vietnam last week.
More than 3,000 Chinese have already returned home from Vietnam by sea and air, reports said at the weekend.
Authorities deployed hundreds of security personnel Sunday to quell the violence and more than 300 suspected perpetrators are being prosecuted, Vietnamese officials said.
There were no reports of any further disturbances in Vietnam on Monday and Hanoi was calm, with authorities scaling back the heavy security presence that had blocked access to the Chinese embassy and other key points in the city.
Activist groups have said several of their members were detained as they sought to demonstrate. Their status was unknown Monday.
- Stay or go? -
Hanoi initially lauded "patriotic" displays by its citizens, but has backpedalled furiously after the violence -- which hit a number of non-Chinese facilities -- badly stained the country's image as a safe destination for sorely needed foreign investment.
Vietnam offers abundant cheap labour and secured $21.6 billion in foreign direct investment last year, up from $16.3 billion in 2012, according to government figures.
"This will definitely have a big impact on the country's image, which so far had been seen as foreign-investor friendly," said a foreign diplomat who spoke on condition of anonymity.
"These actions went way beyond what is acceptable in terms of basic law and order."
Economist Nguyen Quang A said the government must move swiftly and decisively to restore confidence among foreign investors already complaining about corruption, bureaucracy, a lack of legal and regulatory transparency and other issues.
"The government has done some things, but it's not enough," said Quang A.
Authorities have pledged to help enterprises rebuild and restore their operations.
The two nations compete as a destination for investment.
The state-run China Daily newspaper in an editorial Monday raised the prospect of long-term economic damage to Vietnam due to the protests.
"If investors are not confident a government can guarantee a secure investment environment, they will understandably hesitate over making the decision to invest," it wrote.
"To stay or not to stay is now the question for those who already have factories in the Southeast Asian country."
China's foreign ministry has appealed to citizens to avoid travelling to Vietnam.
Several major Chinese travel agencies have suspended their Vietnam tours, Xinhua reported.
"We have also suspended some of our bilateral exchanges," foreign ministry spokeswoman Hua Chunying told reporters at a regular briefing Monday. "We will consider taking further actions in accordance with the development of the situation."
In 2012 Japanese nationals, businesses and diplomatic missions were targeted in violent protests that erupted in several major Chinese cities after Tokyo nationalised disputed islands in the East China Sea.
At the time Beijing was criticised for allowing the protests, which the Japanese government estimated caused damage worth more than $100 million.