The two people who were killed were the helicopter pilot - stunt pilot Pete Barnes, who had worked on films including Bond instalment Die Another Day - and a person on the ground.
It has been reported that the crane driver only escaped because he was late for his shift and had not yet reached his cabin.
Eyewitnesses reported seeing burning wreckage on the road and hearing screams, with a host of calls made to emergency services at around 8am.
It emerged that the helicopter had clipped the crane attached to St George Wharf Tower, before spinning out of control and bursting into flames when it hit the ground.
Visibility around what is one of Europe's tallest resident towers was low, due to mist.
A total of 12 people were injured, although police said it was a "miracle" that the number had not been higher.
More than 60 firefighters were involved in the efforts to bring the blazes under control, also rescuing a man from a burning car.
London Ambulance Service took six people to hospital, with five suffering minor injuries and one having sustained a broken leg, while a number of others were treated at the scene for shock.
Prime Minister David Cameron has been saddened by news of the incident, which happened less than a mile down the River Thames from the Houses of Parliament.
The aftermath, which saw Vauxhall Underground station closed and subsequent disruption on the Victoria line and on roads into the area, was witnessed by a number of MPs.
"I think everyone can see from the terrifying pictures on our televisions this morning, just how quickly the emergency services responded and how brave and how professional they were in the way they responded," Mr Cameron told the House of Commons during Prime Minister's Questions.
River Thames police continue to patrol the waters, amid concerns over the "precarious position" of the damaged crane at the St George Wharf development.
It is understood that the helicopter pilot had tried to divert from his course due to the weather conditions. London Heliport at Battersea received his request via Heathrow air traffic control.
Kevin Hodgson, who worked alongside Pete Barnes on life-saving missions with the Great North Air Ambulance, said: "Pete was as good a guy as you can imagine and one of the best pilots I've ever had the pleasure of flying with."
Police said that the helicopter was flying from Redhill in Surrey to Elstree in Herfordshire.
It has been reported that the intended destination was Elstree Studios, but a spokesman posted on Facebook: "Elstree Studios do not currently have a helipad and therefore the studios were not the intended destination. Our thoughts are with everyone affected."
Authorities have launched investigations into the crash, which left many London commuters shaken.