The Australian beat his Red Bull team-mate Sebastian Vettel in qualifying for the first time all season at Suzuka, claiming his first pole of 2013 in the process.
"It is a nice farewell to have pole at my last attempt at Suzuka, a phenomenal track," said Webber.
"I will never forget the first sector today - it is what we strive for, what our profession is for, so it was a real highlight today."
Vettel's pole shot was hampered by KERS malfunctions during qualifying, but Webber did not think that detracted from his result.
"You have to take them when you get them," said Webber. "Obviously I've attempted to qualify without the weapons before."
Webber is confident his pole will not come under any threat from the officials after an incident with McLaren's Sergio Perez in Q2.
"He backed off, the engineers told me he'd finished his lap so I could pull in front of him," said Webber.
"If he was on a quick lap I would have got out of the way."
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