Bakula appeared in the series as the father of Chuck (Zachary Levi) and Ellie (Sarah Lancaster) but was murdered in the third season.
McPartlin, who plays Devon, has now insisted that Bakula's character Stephen did not fake his own death.
"He's dead, unfortunately," he told Fancast. "And you know why he's dead? Because you have to make that threat real.
"The same thing happened with [Emmett, who was played by] Tony Hale. And it literally breaks our heart."
Chuck returns for a new season on September 20 on NBC.