The group has handed over the ticket hall and platform levels to Crossrail, who will now begin fitting out the station.
Fit-out features include systems needed to operate passenger services such as communications equipment, signalling systems, tunnel ventilation and overhead line equipment.
Canary Wharf Group contributed £150m towards the costs of the new £500m station.
Located in the North Dock of West India Quay, the project is one of the largest Crossrail stations.
The station, retail and park areas are six storeys high, with the development measuring 256 metres long.
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The facility will provide a new link between Canary Wharf and Poplar, currently separated by the North Dock.
It includes links to the Canary Wharf Estate, via Adams Place and the Jubilee line and DLR stations.
Work began on the project in 2009 by creating a 250 x 30 metre watertight dam in the waters of North Dock using a 'silent' piling method.
The station box was then built 'top down,' 28 metres below the water surface to create the ticket hall and platform levels.
Over six and a half years the construction team has driven almost 1,000 piles and pumped nearly 100 million litres of dock water.
Approximately 300,000 tonnes of material was excavated from beneath the dock bed and almost 375,000 tonnes of concrete poured.
Rail Minister Claire Perry said: "The completion of construction at Canary Wharf station is a significant moment for Crossrail, as we move to the next phase of work on this transformational project.
"The station is an impressive, world-class building that will serve millions of customers in this important business district, as well as bringing better and faster journeys across London and beyond from 2018, boosting jobs and economic growth."
(LM/CD)
