From eleventh on the grid, Johnson climbed the order to lead the race as soon as lap 62 and alternated the top spot with Greg Biffle from then on.
Later he slid down the leaderboard following a four-tyre stop under caution on lap 147, while seven cars jumped ahead of him by changing two only.
Johnson was unable to move up again and he had to use a two-tyre pitstop on the last caution to gain track position. Restarting from third with 29 laps remaining he had expected to contend for victory, but instead he lost ground again and could only finish ninth.
"We had such a good car we felt like four [tyres] was really the way to go," said Johnson about his stop on lap 147. "We certainly lost some track position and were in dirty air.
"I don't know, something happened. We were so fast the run before. I had come through traffic a couple of other times. Then the car was really tough to drive, edgy and all over the place so I'm not sure what happened.
"We'll have to get home and look at the car and see what is going on there. It could have just been the track position. So many guys took two and we took four.
"There at the end, we were just trying to get some track position back and I just didn't have the speed that I had the start of the race and had lost a couple of more spots.
"At the end of the day, we finished ninth and that isn't too bad. We hate to see guys we are racing in points ahead of us."
Johnson said the thinking behind his final two-tyre stop was not only to gain track position but also reclaim the lead in the pits to get clean air ahead. However that wasn't the case as both Tony Stewart and Greg Biffle emerged ahead of him due to taking only two new tyres as well.
"We were trying to be the first one out of the pits and went for two and unfortunately a couple of guys took two with us," said Johnson.
"The No. 14 [Tony Stewart, race winner] did a good job of getting away and in to clean air and made the most of it. We were kind of mired in traffic. I was right there with guys on four (new tires) and the guys with four got through and got by and I kind of settled in there in I guess ninth it was.
"Not the finish we were after, we felt like we could have finished better because the first half of the race went so well but ninth is not the end of the world."
Despite losing ground to Mark Martin in the Chase, Johnson says it is early days still in the play-off to start worrying about his rivals gaining a few points on him.
"It is only three races in, the worst finish is ninth and we just don't know what is going to happen," said Johnson. "It is easy to let momentum build for someone or be against someone at this point. But, it is just way too early for myself to even start worrying about it."
Johnson remains second in the Chase, 18 points off from leader Martin.
Biffle still critical of Johnson testMaldonado set for Spain
