But he said trade union action had been the biggest cause of disruption.
The company had made a claim of force majeure (exceptional circumstances), arguing that breaches of its franchise obligations were due to official and unofficial industrial action, including high levels of sickness.
Meanwhile, Southern rail's owners have been fined more than £13 million for poor performance.
Govia Thameslink Railway (GTR) said the settlement was a "fair outcome" and accepted that its performance had fallen short of requirements, causing frustration for passengers.
"Passengers who depend on Southern have been badly let down".
But the RMT union said: "This latest whitewash of the Southern Rail shambles by the government is hardly a surprise when they've been up to their necks in this fiasco right from day one".
However campaigners have pointed out this does not even cover the £20m the Department for Transport (DfT) gave Southern a year ago to help improve services, or the estimated £300m the fiasco has cost the economy.
"So the lesser spotted Secretary of State for Transport, and the lesser spotted DfT, only take back what they have already given and the company - known to passengers who suffer from its mismanagement every day as Southern Fail - does not actually pay the price for failing to deliver".
"No wonder the company are gloating".
This includes the employment of 50 new on-board supervisors on trains to assist passengers and the creation of a fund for specific upgrades that would improve reliability of the railway.
Charles Horton, chief executive of GTR, said: "We are pleased that this issue has been concluded, and accept and are sorry that our service levels haven't been good enough for passengers".
"We absolutely need to modernise in order to increase capacity on this, the most congested part of the UK's network, where passenger numbers have doubled in places in as little as 12 years".
Whilst unions and commuter groups hoped the government would sack the company behind Southern Railway, this was never going to happen as it would pander to ideas of rail nationalisation.
"This has meant we have been running services for more and more passengers while also allowing stations to be rebuilt, platforms extended, track and signalling replaced and new trains and technology introduced too".