Verstappen, who appeared destined to claim pole position for the Saudi Arabian Grand Prix, suddenly slowed during his first run in Q2 and reported a power problem before crawling back to the pits.
The double world champion did not return to the track and will subsequently start Sunday’s race 15th, while teammate Sergio Perez went on to take pole.
Speaking after qualifying, Horner said Verstappen’s problem “looked like” a driveshaft failure.
“[A drive shaft issue] is what it looks like at the moment,” Horner told Sky.
“We have obviously got to get into the car and see exactly what has happened.
“A great shame because that one lap he did in Q1 would have put him fourth on the grid.
“But nonetheless, we have got a quick race car and I am sure we he will race well tomorrow.
“The lap from Checo, the first lap in Q3, was phenomenal, so I am delighted for him to get his second pole today.”
Red Bull fitted a new gearbox in Verstappen’s car after the Dutchman encountered issues during Friday practice in Jeddah.
Asked if there was any reliability concern heading into the weekend, Horner said: “There wasn’t a concern coming into the race, it was just part of our strategy of introducing parts into the pool.
“Something obviously has happened there and we need to get to the bottom of it and understand it and make sure that it doesn’t happen tomorrow.
“It is a tough race here, it is going to be a matter of staying out of trouble.
“There is going to be plenty of action, plenty of carnage and it should provide an exciting race hopefully.
“It is a great opportunity for Checo, important to convert that, and we are going to have two different races going on in the Grand Prix tomorrow.”