The RMT union began the 72-hour walkout on New Year's Eve.
The action prompted warnings of widespread disruption for travellers during new year celebrations.
Southern's parent firm Govia Thameslink (GTR) is in dispute with both the RMT and Aslef unions. Another strike is set for 9 January.
The planned six-day strike involves train drivers from both unions. Most routes are expected to have no services.
The train drivers' union Aslef is continuing with a ban on overtime which is adding to the disruption.
The RMT and GTR have said they are available for talks and Aslef took part in negotiations in December at conciliation service Acas, but discussions ended without a deal.
RMT leader Mick Cash called on Transport Secretary Chris Grayling to make it his new year resolution "to get in a room with the unions and his contractors to sort out the current shambles".
Mr Grayling said it was frustrating the unions had decided to start a new year with the continuation of an old strike.
He said: "We are investing record amounts in improving our railways and we need everyone in the rail industry to work together to deliver for passengers.
"Now the unions need to come back to the negotiating table. Only they can end this misery for rail users."
Southern's deputy chief operating officer Alex Foulds said: "Our door remains open for meaningful talks."
The politics behind the Southern rail dispute
What's the Southern Rail strike about?
How bad have Southern rail services got?
The Association of British Commuters said disruption had caused health problems, forced people to move house and lose jobs.
The campaign group surveyed about 1,000 passengers and said the results highlighted the extent of suffering as a result of the "breakdown" of Southern services, with delays, cancellations and overcrowding.
Calling for government intervention, a spokesman said: "Thousands of people are now at breaking point."
The Department for Transport has said the dispute is between Southern and the unions and "not something the government is involved in".

The Marine Conservation Society said more than 8,000 bottles were picked up during its Great British Beach Clean Up in September, up 43% on 2014.
It wants deposit return schemes, which give money back to people who return empty bottles, to encourage recycling.
More than 6,000 volunteers collected and recorded litter along 340 beaches across the UK.
The MCS said putting a charge on the bottles of up to 20p, which gets refunded when they are returned, would change behaviour, and called for the UK government to explore the potential of such a scheme.
Lauren Eyles, the charity's Beachwatch manager, said: "The bottles we find on beaches are either dropped directly on to the beach, blown from land or sea, or end up there via rivers.
"The more we use as a nation, the more we'll see ending up on our shores."
The survey also found:
All countries within the UK saw an increase except Wales, where levels dropped after a record rise the previous year, the MCS said.
England saw record levels of litter across 189 beaches, with highest levels of rubbish - averaging 5,170 items per kilometre - in the South West.
The Channel Islands had the lowest levels of litter for the UK, but rubbish still increased by a fifth (22%) compared with 2014.

The 20-year-old Slovak has yet to play for Fulham's first team, but made 17 appearances in the National League on loan at Welling last term.
Rodak, who has represented his country at youth level, will go straight into Accrington's squad for their League Two fixture against Cheltenham on Saturday.
Stanley are 20th in the table, four points above the relegation zone.
Find all the latest football transfers on our dedicated page or visit our Premier League tracker here.

Police were called to Station Road, Wood Green, at about 03:20 BST after receiving reports of a stabbing outside the Jolly Anglers public house.
Paramedics treated the man, named by police as 33-year-old Vincent Harvey, but he was pronounced dead at the scene.
No arrests have been made and the Met have appealed for witnesses.
Det Ch Insp Noel McHugh said there was "a large number of people in and around the Jolly Anglers pub at the time Vincent was stabbed".
"It is vital that anyone who saw this incident, or the events leading up to the incident, get in contact with police," he said.
A strike by conductors on Southern rail has entered its second day as a long-running row about the role of guards on new trains continues.
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Conservationists say they found 160 plastic bottles for every mile of UK coastline cleaned last year.
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Accrington Stanley have signed goalkeeper Marek Rodak on loan from Fulham until the end of the season.
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A murder investigation has been launched after a man was stabbed to death outside a busy north London pub.