The world number three, who was five shots clear after the first two rounds, birdied the first and fourth holes to move to 13-under before play was suspended at the Royale Jakarta Golf Club.
The Englishman, who is defending his title at the course and finished third at the US Masters two weeks ago, will return early Sunday to complete his round.
"The suspension stopped a bit of momentum going but if it is dangerous weather out there then it is the safest thing to do," he said, according to a press release from the Asian Tour.
"I'm in a good position and I'll come out tomorrow and try to keep the form up."