Counter-terror police arrested the women aged 26 and 27 "on suspicion of being involved in the commission, preparation and instigation of acts of terrorism", London's police headquarters said.
A Scotland Yard spokeswoman would not comment on whether the arrests were in connection with foreign fighters travelling to fight in Syria, across the border from Turkey.
Officers "acting on intelligence" stopped the 26-year-old at London Heathrow Airport's Terminal 5 as she was preparing to catch a flight to Istanbul, the force said in a statement.
The 27-year-old woman was arrested several hours later at a house in northwest London.
The pair remain in custody and detectives are searching two premises in London.
"Both arrests were intelligence-led and not in response to any immediate threat or risk," the police statement said.
British police have arrested a number of people under anti-terror laws in recent months on suspicion of going to Syria to fight with jihadi groups.
Two men arrested on Monday at Heathrow on suspicion of terror offences after arriving on a flight from Istanbul remain in custody.
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