The revamp of the 550m long tunnel runs below the Royal Docks next to ExCeL London, was one of the most complex jobs on the project.
The tunnel was built in 1878 and has not been in passenger use since December 2006.
Contractor Vinci took the job to deepen, strengthen and widen the structure and remove 135 years of coal and soot from the steam trains that originally used the tracks.
Last summer, 13m litres of water were drained from the dock that runs above the tunnel to allow Crossrail workers to access the structure from above.
The rail tunnel originally served the Royal Docks when they formed the largest enclosed docks in the world, serving large ships from all over the globe. It survived a hit from a bomb during WW2 and is the only existing tunnel that will be re-used for Crossrail.
Linda Miller, Connaught Tunnel Project Manager said: “It’s great to know that, thanks to our work, this old tunnel will once again have a vital role to play in London’s transport network.”
The tracks, overhead cables and communications systems required to run the trains will begin to be installed next year. Up to 12 trains an hour in each direction will pass through the tunnel, reducing journey times and supporting the wider regeneration of the Royal Docks.