More than 20 people were killed yesterday in the latest battles between factions seeking to control Tripoli airport on Sunday, while fighting led to a huge fire raging nearby at the city's fuel depot.
Staff at the UK embassy were among those seeking sanctuary in Malta following the so-called "assisted departure" operation.
It is thought the Plymouth- based HMS Enterprise moored just off the Libyan capital city and dispatched a smaller vessel to fetch the evacuees.
Up to 300 Britons are believed to be in Libya. Many of the consular staff were evacuated last Monday but the ambassador and core staff remained, although they will now also return to the UK.
Since the overthrow in 2011 of Colonel Muammar Gaddafi by rebels supported by British and French air-strikes, the country has descended into a state of lawlessness as rival militias struggle for power and wealth
In the last few days, sporadic fighting between rival militias has spread northwards in the capital, including into the area where the British embassy is based.
Any Britons unable to take advantage of the naval operation have been told they should find their way home on commercial flights, with limited departures from Misrata and Maitega airports.
On Wednesday, British Airways suspended flights to and from Tripoli up to and including tomorrow due to the security situation at the country's main international airport.
A Foreign Office spokesman said it planned to temporarily suspend operations at the British embassy following the assisted departure. It said it would not be able to offer consular assistance after today.
HMS Enterprise's commanding officer, Commander Mark Vartan, said: "This is a period of uncertainty for UK citizens based in Libya but we have been proud to play our part in enabling their move to safety.
"My ship's company have adapted to the challenge superbly, making as much space as possible and providing essential food, shelter and security for the journey."
Defence Secretary Michael Fallon said: "I thank the crew of HMS Enterprise for their support and professionalism in carrying out this important task."
Rival factions allied to brigades from the towns of Misrata and Zintan have been fighting for nearly three weeks for control of Tripoli's airport in the worst violence since Gaddafi's fall.
The city was quieter yesterday morning except for sporadic blasts. But eight gas tanks hit by a rocket on Saturday at a fuel depot near the airport were still burning, sending a huge pall of smoke up over the capital.
"Tripoli's hospitals received 22 bodies on Saturday and 72 people were wounded," Libya's government said in a statement yesterday.
"Mediating committees are still trying to stop the violence and return Tripoli to normal. They have faced difficulties because of the stubbornness of the militias attacking the city."
Most Western governments have evacuated their embassies, fearing that Libya is sliding back into civil war.