The government said the fine for the parent company Govia Thameslink would have been higher, but most of the delays had not been Southern's fault, with strikes and unprecedented levels of sick leave being blamed.
Instead of removing the franchise from GTR following its so-far disastrous tenure, transport secretary Chris Grayling ordered the company to spend £13.4m on improving services after concluding that Southern's performance was "not good enough" and industrial action does not fully explain such a poor performance.
The fine money will be invested in improvements to services - including £4million to fund 50 on-board supervisors over the next two years.
GTR is also expected to submit a plan to the Department of Transport (DfT) on how it will improve services for passengers.
In a letter to Charles Horton, the chief executive of GTR, transport secretary Chris Grayling wrote: "Performance on Southern has improved dramatically since Christmas, as the disruption from union activity has decreased".
"No wonder the company are gloating".
It says Southern Rail has consistently failed to employ enough drivers to deliver the services it promised, in its franchise application, to provide to passengers and is, therefore, dependent on the goodwill of staff to volunteer to work overtime.
The report suggested that poor industrial relations were the main cause of disruption to services, but Mr Grayling added that DfT officials had "determined that this does not fully explain the poor service that passengers received".More news: Kellyanne Conway sparks torrent of memes with latest interview gaffe
To call three days of strikes spread across a week is a deliberate move to cause maximum disruption for passengers.
"We run the most congested network in the United Kingdom where passenger journeys have doubled in the last twelve years.
Chris Grayling has propped up the basket case Southern rail operation from the off".
Go-Ahead said the agreement has resolved financial uncertainty relating to past industrial action, and will allow GTR to focus on improving services for customers.
Lianna Etkind, of the Campaign for Better Transport, described the money being spent by GTR as "too little, too late".
In the past 12 months less than three-quarters (74%) of Southern mainline and coast services met the industry punctuality target of arriving at their terminating station within five minutes for commuter services and 10 minutes for long-distance journeys.
The average score for all operators across Britain was 88%.