Network Rail (NR) has agreed to create a £4.1 million fund to directly benefit passengers after being threatened with a fine for its poor planning of upgrades.
In August the Office of Rail and Road (ORR) announced it could impose a financial penalty of £2 million on NR in the wake of severe disruption at London Bridge station.
Chaotic scenes at the station made headlines in December 2014 and the problems continued into this year.
The ORR found that NR had "failed to engage adequately" with train operators over the impact improvement work would have on passengers.
This led to Southern and Govia Thameslink Railway missing punctuality targets for commuter routes serving London Bridge last year.
The operators accounted for a third of delays and almost half the cancelled and significantly-delayed services in England and Wales.
The ORR has accepted an offer from NR to avoid its fine in return for creating a fund for passengers on Thameslink, Southern and Gatwick Express services.
NR said this will lead to extra staff at stations served by those operators, including 15 more at London Victoria.
There will be improvements to information displays at stations and 20 new track workers based at Brighton and Croydon to respond quickly to problems.
The company is also deploying up to four times more security patrols at stations in Sussex in a bid to reduce delays caused by trespassers.
NR managing director Phil Hufton said: "Passengers expect and deserve a high standard of service, and we accept that we fell short for those travelling on Southern and Thameslink services last year.
"Since then we have invested £11 million to improve the railway around London Bridge and elsewhere in the region, and performance has increased as a result.
"This extra £4 million will continue the improvements we have already made and it is good news for passengers that the ORR has recognised this as a positive and practical alternative to a fine."
ORR chief executive Richard Price said: "We welcome Network Rail's commitment to improve passenger services.
"The new fund will enhance the service for passengers affected by this poor performance."
Work to renovate London Bridge station and the railway around it is due to be completed in 2018.
NR said it will lead to better reliability and more frequent rail services across the capital.
David Sidebottom, passenger director at independent watchdog Transport Focus, said: "We welcome the regulator taking action and it is a positive step that this money will be spent on schemes to directly improve the experience of passengers.
"Passengers just want a railway they can rely on. However, where there is further disruption, industry must be more proactive in letting passengers know when they are able to claim compensation and making it simple to do so."
Rail Minister Claire Perry said: "I know that customers on this part of the rail network haven't always received the high-quality service that they deserve, which is why our plan for passengers is focussed on improving performance.
"I am pleased that Network Rail and ORR have agreed a package of much-needed improvements that will directly benefit customers, and I expect the industry to continue to work together to identify whether further improvements can be made."