By the time he returned it was too late to save the plane, two people close to the investigation told news agency Reuters.
They said that investigators were examining the Flight Augmentation Computer (FAC) recovered from the Airbus A320, and that the captain had taken the "very unusual" step of disabling the system.
"You can reset the FAC, but to cut all power to it is very unusual," said an A320 pilot, who chose to remain anonymous.
"You don't pull the circuit breaker unless it was an absolute emergency. I don't know if there was one in this case, but it is very unusual."
Experts said the loss of the FAC would not directly alter the trajectory of an aircraft but that it would remove flight "envelope protection", which prevents a pilot from taking a plane beyond its safety limits.
Shortly after the pilot is believed to have disabled the FAC, Flight QZ8501 went into a sharp climb from which investigators have said it stalled or lost lift.
"It appears he [the co-pilot] was surprised or startled by this," said a person close the investigation, referring to the decision to cut power to the FAC.
"The co-pilot pulled the plane up, and by the time the captain regained the controls it was too late."
This contradicts reports earlier this week which claimed the co-pilot was in control at the time of the crash, after the plane's flight data recorder was analysed.
AirAsia said it would not comment while the matter was under investigation by the National Transportation Safety Committee (NTSC) of Indonesia. Tatang Kurniadi, chief of the NTSC, told Reuters there had been no delay in the captain resuming the controls, but declined further comment.