Flynn was placed in caretaker charge following John Toshack's departure but has suffered defeats in his only two matches at the helm.
A 1-0 loss at home to Bulgaria last Friday was followed by a 4-1 reverse in Switzerland on Tuesday, with the Football Association of Wales now set to make a decision before the next qualifier.
Flynn has expressed a desire to keep the job and Bale believes he deserves more time after being encouraged by many of the signs over the past few weeks.
"I think he has been fantastic, training has been a lot more lively," the Tottenham wide man told Sky Sports News.
"The performance wasn't bad out there at all. We passed the ball around and created a lot of chances.
"He's done a great job and he's had such a short time that it's hard for him to do a lot.
"There were a lot of positives to take from the game so hopefully he can get it."