More than a hundred trees fell across train tracks leading to the capital, meaning most operators cancelled and delayed morning services.
Services on the Overground were cancelled until lunch time, and parts of the Piccadilly, District, Northern and Bakerloo Underground lines were also put out of action by track obstructions.
Operators hope to run normal services today. The Eurostar, which cancelled a handful of morning journeys, was running normally last night.
Heathrow axed 130 flights yesterday, while Gatwick, whose runways are less busy, managed to fly all but six of its scheduled services.
Four people died in the gales across southern Britain yesterday including a 17-year-old girl killed when a tree fell on a static caravan in Kent, and a couple who were found dead in a suspected gas explosion caused by a felled tree in Hounslow.
Power cuts hit almost half a million properties during the day, with more than 100,000 still without electricity last night, UK Power Networks said.
The Dungeness nuclear power station in Kent was closed as a precaution ahead of the storm.
And the Cabinet Office on Whitehall was evacuated after a crane crashed into the building.
The worst of the storm has already passed over Britain into the Netherlands, Denmark and Sweden.
Insurers were starting to count the cost of the storm yesterday, though some said the damage inflicted by St Jude was less severe than the storms of 1987, which cost £2.2bn.
Analysts at Oriel Securities said it would be “very surprising” if the weather added more than two percentage points to insurance firm’s combined ratios, which measure premiums written against claims paid.
Traders reported thin volumes on the London Stock Exchange yesterday, suggesting many in the City opted to stay home rather than brave the commute.