Scotland Yard said a 25-year-old British national of Turkish origin had been charged with offences contrary to Section 5 of the Terrorism Act 2006 and Section 58 of the Terrorism Act 2000.
A British national of Algerian origin, also 25, has been charged under Section 58 of the Terrorism Act 2000 and with a further offence contrary to the Identity Documents Act 2010.
Both men were arrested last Sunday following a swoop where marksmen used special ammunition to stop a car on Mansell Street, near the Tower of London.
They will appear in custody at Westminster Magistrates' Court tomorrow.
The British national of Turkish origin is accused of preparing a terrorist act with the intention of committing or assisting another to commit such an act.
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Both men are accused of making a record of information of a kind likely to be useful to a person committing or preparing an act of terrorism or possessing a document or record containing information of that kind.
The British national of Algerian origin is also charged with possession of false identity documents with improper intention.
They were arrested following the "hard stop" on suspicion of the commission, preparation or instigation of acts of terrorism.
Police had been granted additional time to question until today at a south London police station.
Two other men arrested as part of the same operation were freed without charge yesterday.
One is 28-year-old British national of Azerbaijani origin detained by officers on upmarket Westbourne Grove in west London, while the other is a 29-year-old British national of Pakistani origin arrested in Peckham, south-east London.
A spokesman said officers had completed searches at six addresses in London and also on two vehicles as part of their investigation.