She slid down a rope a second-storey dental surgery where she was undergoing orthodontic treatment and an accomplice whisked her away on a motorcycle as passers-by looked on.
Her escape was a great embarrassment for the Colombian prison system.
CCTV footage of her sliding down a red rope and landing on the pavement went viral. Many Colombians questioned why she had been allowed to leave the prison and why the guards had not entered the surgery with her.
The head of the prison where Merlano had been held was fired for authorising her request to see the dentist at a private surgery.
Miguel Domínguez, who heads Venezuela's Faes special forces, announced the capture on Instagram, where he posted a photo of the fugitive senator and a Colombian national who allegedly also entered Venezuela illegally.
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According to Mr Domínguez, Merlano was captured in the Venezuelan city of Maracaibo "after arduous investigations carried out by Faes officials". He said she would be handed over to the Venezuelan prosecutor's office.
It is not clear if Merlano will be extradited to Colombia. Relations between the two countries have been tense for years.
Colombian President Iván Duque does not recognise the government of Venezuelan leader Nicolás Maduro as legitimate. Last week he received opposition leader Juan Guaidó - who proclaimed himself acting Venezuelan president last year - with full presidential honours in Bogotá.