This follows last week's Cabinet reshuffle by President Jacob Zuma, which saw Peters lose her job to Joe Maswanganyi.
The office of the ANC chief whip says the resignation was effective from 31 March.
The former minister says she's been waiting for this opportunity to leave due to the uncertainty around her job over the last two years.
Peters says she is not disappointed by Zuma's final decision.
"I've been living in a situation of uncertainty because every now and then it would be said: 'It's a reshuffle, it's a reshuffle.'"
