Mick Whelan, ASLEF's general secretary, said: "The agreement means we will have a second safety-trained person on every train covered by this agreement except in exceptional circumstances".
"The agreement also confirms the terms and conditions under which our members at Southern are employed".
Last year ASLEF joined the RMT union's industrial dispute over the further extension of DOO on the Southern network by Govia Thameslink Railway.
Aslef members backed the agreement, which includes a pay rise of 28.5% over five years.
The Office of Rail and Road has said of driver-only operation: "Our inspectors are satisfied that with suitable equipment, proper procedures and competent staff in place, it is a safe method of working".
Govia Thameslink Railway Chief Operating Officer Nick Brown said: "This dispute has been hard for our passengers in particular, and we are pleased that we can now move ahead and deliver stability by finally concluding this deal with ASLEF". The on-board service concept has been welcomed by our passengers across the board.
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More train stoppages have been scheduled over the next few weeks, including match day on November 14, as workers protest to demand a 3.75% pay increase.
The dispute on Southern began in April of 2016, and has resulted in a series of strikes on the network which have created travel disruption for thousands. Greater Anglia plans to run a full service as most trains do not have guards, while Southern said for the most part it will be "business as usual", with some alterations planned.
"Driver-only operation has been operating safely for 32 years and now accounts for over a third of the United Kingdom rail network".
The stoppages by members of the Rail, Maritime and Transport union (RMT) over the introduction of driver-only trains will be staggered over the coming days and will severely affect the services of five rail operators.
RMT General Secretary Mick Cash said: "This shoddy deal, sponsored by Theresa May and Chris Grayling, extends and institutionalises discrimination against disabled and older people".
The letter said: 'I remain concerned that in the event of a train evacuation, derailment or incapacitated driver, the absence of a guard to assist could leave passengers at risk.