That's the way it happened. It wasn't the fastest car that won the pole...it was just some random car caught in the draft that received the number one starting spot on the grid. It just so happened that Jeff Gordon crossed the line going faster at that time. Good for him but he didn't win it. He was the lucky one.
The knock out qualifying method works for other racing sanctions like Indycar and Formula One, etc. but, Nascar is so dependent on the draft it's not at all representative of who has the fastest car. I see another rule change coming in the near future.