Transport minister Andrew Jones said the changes would deliver a better standard of services.
About 20 million car journeys will be made between Thursday and Monday.
The driver, Alfred Dorris, was arrested at the scene and questioned on suspicion of manslaughter before being bailed until May.
The proposed north-south rail line would run across London between Hertfordshire and Surrey.
The imbalance in transport infrastructure investment between London and the rest of England is "set to get even worse", a study has warned.
A coroner has demanded Transport for London do an "urgent review" of the blue paint used on cycle superhighways after a motorcyclist died earlier this month.
The action comes days ahead of a 24-hour strike next Monday.
RMT and Aslef union members both walked out for 24 hours until 9pm on Wednesday.
The Tube strike started at 9pm on Tuesday and halted the Waterloo and City line and affected the Central line.