The teenager was detained after Scotland Yard Counter- Terrorism Command officers executed a warrant at Thornton Heath area of the city at around midnight.
All six arrested remain in custody at a south London police station.
Police have begun a search of the property where the teenager was arrested under Section 41 of the Terrorism Act.
Commander Dean Haydon, head of Scotland Yard's Counter- Terrorism Command, said: "This continues to be a fast-moving investigation.
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"We now have six males in custody and searches are continuing at five addresses. Detectives are carrying out extensive inquiries to determine the full facts behind the attack."
The suspects have not been named officially until they go on to be formally charged but the 21-year-old has been identified locally as Syrian refugee Yahyah Faroukh.
All arrests have been made under Section 41 of the UK's Terrorism Act.
A homemade bomb partially exploded in a train at Parsons Green station in west London, injuring 30 people during rush hour on September 15.