Maldonado had been due to continue with the British-based outfit alongside Jolyon Palmer, son of former Formula One driver Jonathan Palmer.
Maldonado confirmed his departure on Twitter.
“Today with the biggest humility I inform you that I won’t be on the grid at the start of the 2016 season. Thanks for all the messages of support, passion and concerns about my future.
“I’m very thankful to God, my family, my sponsors, my friends, my fans and everybody who has helped me materialise this dream of having represented Venezuela in the pinnacle of motorsport. See you soon!”
According to Autosport, 23-year-old Magnussen will be confirmed as Maldonado’s replacement on Wednesday.