The council imposed the fine on the water company for the delays, but Thames took the unusual step of making Skanska pay the full fine.
The work was carried out between June and October last year and has resulted in the company overrunning on four sites by a total of 136 working days.
The company was fined using an interactive mapping system that monitors works going on around London.
A Thames Water spokesman said: “We are really sorry for these overruns. These works were not managed to our satisfaction. As a result, our contractor has agreed to incur the majority of the fines.
“Ideally we wouldn’t have to dig up the streets at all. But our 150-year-old, leaky cast iron water pipes desperately need replacing.
“Our mains replacement work will deliver long-term benefits, greatly reducing leakage and the amount of disruption caused by emergency work in future years.”