Govia Thameslink Railway (GTR) must contribute £15m towards improvements in services for rail passengers and will make no profit in 2018, the Department for Transport (DfT) has said.
The company has already spent a similar amount in passenger compensation after chaos following May's new timetables.
The DfT said: "Performance after the May timetable change was unacceptable."
MPs also said that Transport Secretary Chris Grayling should have been more proactive in preventing the problems.
In a scathing report on May's timetable changes, the Transport Committee said "genuine change" was needed to restore trust in the railways.
Although Mr Grayling had not been fully informed, this could not absolve him of all responsibility, the MPs said.
It was extraordinary that no-one took charge of the situation, they said.
Mr Grayling admitted mistakes had been made, telling BBC Radio 4's Today programme: "I accept responsibility for myself and my department not asking tough enough questions."
But he added: "At no point did I get the information that I would have needed to intervene."
The DfT decided not to strip GTR - which is 65%-owned by UK transport company Go-Ahead - of the franchise, because it said that would "cause further and undue disruption for passengers, and is not an appropriate course of action".
But its sanctions on the company mean it will make a reduced profit for the rest of its time in charge.
The DfT said the action "holds GTR to account" and added: "The department will continue to monitor closely the performance of GTR, particularly during the upcoming December timetable change.
"These measures do not make GTR immune from further sanctions in the event of any subsequent failure to perform."
Changes to the national rail timetable happen each May and December and are often relatively minor tweaks.
But last May, after major infrastructure works, a far bigger timetable overhaul was introduced, involving 43,200 individual changes and affecting 46% of passenger services.
MPs said its implementation was chaotic and resulted in inconvenient, costly and potentially dangerous disruption for passengers across the north of England and in London and the south.
The chaos was partly caused by the "astonishing complexity" of a fragmented railway in which interrelated private train companies, operating on publicly-owned and managed infrastructure, have competing commercial interests, the report says.
It concludes that no-one took charge. Mr Grayling had the ultimate authority to judge trade-offs between competing commercial interests and he should have been more proactive, the report says.
"There was extraordinary complacency about protecting the interests of passengers, who were very badly let down," said committee chairwoman Lilian Greenwood. "It is extraordinary, and totally unacceptable, that no-one took charge of the situation."
Mr Grayling has announced a year-long independent rail review, chaired by Keith Williams, deputy chairman of John Lewis Partnership and former chief executive of British Airways.
Mick Cash, leader of the Rail, Maritime and Transport union, described the report as "devastating" and laid the blame on "disastrous fragmentation of our railways" and Mr Grayling.
Anthony Smith, chief executive of watchdog Transport Focus, said: "This industry knows it must deliver a smooth set of changes when the next round of timetable changes takes effect this Sunday.
"They must show they've learned lessons after a torrid summer of timetable crisis, and are acting to improve performance."
A Department for Transport spokesman said: "We have already worked with the industry to deliver special compensation schemes on Northern, TransPennine Express and GTR, which provides the equivalent of up to 8% of the cost of an annual season ticket for those most severely impacted.
"The disruption following the May timetable change demonstrated that significant change is required in the rail industry. That is why we launched the Williams review to consider all parts of the industry in order to put passengers first, with reforms to begin from 2020."
Govia Thameslink Railway was one of the train operators whose passengers were badly hit during the disruption. Chief executive Patrick Verwer said the firm has already processed compensation claims for 68,000 season ticket-holders, with the deadline for claims extended to 31 January 2019.
He said: "Since July, services on Thameslink and Great Northern have become more stable and reliable."