The German set a new track record to heap more misery on his Mercedes rival who will start from 14th on the grid come Sunday.
Hamilton’s car got stuck in fourth gear causing him to bow out of Q1, despite his best efforts of pushing the car back to the pit lane before the end of the session.
Vettel, meanwhile, took pole position in Hockenheim as he looks to pull away in the race for the title.
The Ferrari man admitted his main goal was to ensure he finished on top ahead of his home Grand Prix.
But the championship leader did admit he felt for Hamilton.
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“Obviously we saw but I don’t know what exactly happened,” Vettel said about his rival’s incident.
“It doesn’t really matter. We will see what happens tomorrow. Obviously you look after yourself. For me it was a good session and everything went smoothly.
“You always try to push the limits. Don’t wish anything bad or technical issues to happen to anyone.
“It’s a shame to see him go out, and I mean it.
“But you look after yourself. The most important part of the weekend is the race.”
Vettel admitted he had a great feeling about his car during practice and was confident that he could grab another pole this weekend.
“In qualifying the car was a pleasure to drive,” he continued.
“Some days you can feel already when you go out, and do your first flying lap, that you have something in your hands that you can play with.
“That’s the feeling I had today. And from there it just got better. It was more about tuning myself. In the sessions before sometimes I did get the laps together, sometimes I didn’t – I was trying different things.
“I knew in Q3 I could get quite a bit out of the car and myself, and made it work. Really happy, both laps on the limit.
“Then the adrenaline kicks in. It’s quite a good feeling when you get everything right. Really, really happy with the car and the work we’ve done overnight.”