A 24-hour walkout by members of the Rail, Maritime and Transport (RMT) union, in protest at the introduction of driver-only trains, ended at 11:00 BST on Wednesday.
Southern warned passengers to expect "difficult and frustrating" journeys throughout the day.
Two further strikes have been announced for 10 May and 12 May.
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The RMT confirmed it would attend talks with Southern "over the guards jobs and safety dispute" on Friday.
Dyan Crowther, chief operating officer for Southern owner Govia Thameslink Railway, told BBC Sussex: "We are very pleased to hear that and we look forward to meeting the RMT".
Southern said some routes were again suspended or reduced with 700 fewer services across Sussex and east Surrey.
Ms Crowther said the timetable would not return to normal until Thursday as they needed to get rolling stock and staff into the right position.
Paul Barker, a commuter from Rye, normally catches a Southern train to Ashford then a high-speed service to St Pancras.
He said he worked from home on Tuesday but went to Robertsbridge on Wednesday to catch a Southeastern service to London.
He said: "It was standing room only from Frant, but you cannot take two days off work".
RMT general secretary Mick Cash said: "This dispute is about safety. The company, with an eye on ever-fatter profits, is prepared to axe the guards on some of the most overcrowded and potentially-dangerous services."
The company said there would be no job or pay cuts but the planned changes would make conductors more visible while drivers would operate doors.
It accused the RMT of "scaremongering" and said "driver-only operation is a safe, proven way of working" which had been used "on 40% of trains across the Southern network for 25 years".

Fifa president Sepp Blatter announced plans last week to form an 11-person panel to review football's scandal-hit world governing body.
Domenico Scala had earlier said he would only lead the taskforce if he is guaranteed full independence.
The Swiss businessman is already the independent chair of Fifa's audit and compliance committee.
Scala was believed to have been prepared to lead the taskforce, after meeting presidents of three of Fifa's six continental confederations.
But a spokesman for Scala told BBC Sport: "Domenico Scala never applied for such a chairmanship."
He added that the post would only be considered "under the strict condition" that "independence was guaranteed".
As well as an independent chair, the taskforce will have two representatives from the AFC (Asia), CAF (Africa), Concacaf (North, Central America and the Caribbean) and Uefa (Europe), as well as one representative from each of Conmebol (South America) and the OFC (Oceania).
In a statement, Fifa said representatives from federations would not necessarily have to be "members of the football community" and the confederations could decide that themselves.
Blatter, who has announced his intention to stand down as president, has said presidential term limits and integrity checks for top officials are potential areas of reform.
Recommendations are due to be presented at the next meeting of Fifa's executive committee in Zurich on 24 and 25 September.
The prospect of Scala leading an independent review of Fifa was described as "laughable" by campaign group New Fifa Now.
And Alexandra Wrage, who resigned from Fifa's independent governance committee in April 2013 in protest at a lack of meaningful action, said even an independent chairman of the reform taskforce "can't work".
She told BBC Sport: "The process needs to be taken out of Fifa's hands. Short of that, it's another reform dead-end."
Blatter's resignation on 2 June followed the arrest of seven Fifa officials as part of a United States investigation that saw 14 people indicted on corruption charges.
A separate criminal investigation by Swiss authorities into how the 2018 and 2022 World Cups were allocated is also under way.

Organisers said hundreds of revellers took part in the celebration of the coming of summer.
Event co-ordinator Sara Thomas said Beltane was an ancient tradition with a modern twist.
The modern Beltane Fire Festival has run since 1988. This year's celebration included drummers, fire dancers, physical theatre, and a bonfire.
Talks to prevent a further strike by Southern rail conductors are to be held on Friday.
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Fifa has said its reform taskforce will be chaired by an independent person from outside of football.
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Thousands of people gathered on Calton Hill in Edinburgh on Thursday night for the Beltane Fire Festival.