Bay and Wahlberg previously worked together on "Pain and Gain," which hits theaters this April.
"Mark is awesome. We had a blast working on 'Pain and Gain' and I'm so fired up to be back working with him. An actor of his caliber is the perfect guy to re-invigorate the franchise and carry on the Transformers' legacy," Bay said in a statement on his website.
Bay will direct the next installment in the "Transformers" series, which will begin shooting next spring.
The filmmaker did not say what part Wahlberg will play or which other actors might co-star alongside him.