The second "bomb" was discovered in a Mercedes that had been parked illegally in London's West End and towed to an impound lot near Hyde Park.
The first device was discovered when an ambulance crew treating a person at the Tiger Tiger nightclub in Haymarket called police explosives experts after noticing smoke issuing from a Mercedes outside the nightclub just before 02:00am (01:00 GMT).
Police later said that inside the car they found "quantities of petrol" and a "large number" of nails.
A large area near Piccadilly Circus, packed with tourists, theatres, restaurants and pubs, was sealed off after the car was found and office workers were unable to enter their buildings at the start of the work day.
Police plan to examine footage from closed-circuit television cameras in the area, hoping to track down those involved.
Speaking before the second device was found, Gordon Brown, UK's new prime minister, said the alert was a fresh warning of the threat faced by London.
"The first duty of a government is the security of the people and as the police and security services have said on so many occasions we face a serious and continued security threat to our country," he said.
Steve Park, a security analyst, told Al Jazeera that it was not clear if the bomb had been intended for the night club as there were other potential targets in the area, but he said the bomb had been intended to injure as many people as possible.
Park said: "The bomb was made for massive collateral damage ... it's at the very bad end of making bombs."
Jacqui Smith, UK's new interior minister, called an emergency meeting of officials, saying the attempted attack was "international terrorism".
"We are currently facing the most serious and sustained threat to our security from international terrorism," she said.
"This reinforces the need for the public to remain vigilant to the threat we face at all times."
Security around parliament was stepped up, with police body-searching drivers of vehicles entering the area.
Earlier in the year, a number of people were jailed for life for plotting to attack a number of targets in Britain, including a prominent London nightclub.
Last year in November, a man was jailed for 30 years for plotting to detonate limousines packed with explosives near landmarks in London and New York.
Friday's bomb scare came almost two years after a series of co-ordinate suicide bomb attacks on London's transport network killed 52 commuters, the first suicide bombings in Western Europe.