The three-time Japanese Grand Prix winner reckoned that slowing for other riders cost him at least 0.8 seconds - meaning he potentially missed out on second place.
"I am a bit upset about the last qualifying lap, as I hit a lot of traffic and lost eight tenths of a second in the third section," Capirossi said.
But the Italian is very upbeat about his race prospects and believes he can produce his most competitive race performance since joining Suzuki.
"I am really pleased with the bike and it is probably the best we have had a bike set-up for race distance," said Capirossi, who is chasing a fourth consecutive Motegi win.
"We hope that we will have the same conditions in the race tomorrow as we had this afternoon and then we will have to see what happens."
Team boss Paul Denning was delighted with Capirossi's performance.
"Loris pushed to the absolute limits in qualifying today and it was great to see his confidence back at a high level," said Denning.
"A front row start would have been nice, and it looked really possible, but a huge time loss on his last lap caused by traffic ruined the chance of that.
"As he said yesterday it's going to be tough to win his fourth successive Motegi GP, but nobody on the grid will be trying any harder tomorrow."
Capirossi's teammate Chris Vermeulen only qualified 12th, but was relatively satisfied with his position having traditionally struggled at Motegi.
"That has been the best session of the weekend so far and (crew chief) Tom (O'Kane) and the team have done a fantastic job to get the bike set up for here," said Vermeulen.
"The race tyre pace improved a lot throughout today, but unfortunately I made a bit of a mistake on my last qualifying tyre. If I hadn't perhaps the time would have been a bit better than it was.
"It is the best qualifying I have done at Motegi and I am definitely enjoying the track a lot more, so hopefully the race result tomorrow will reflect that."
Suzuki are running a third bike for local rider Kousuke Akiyoshi this weekend, but he has struggled for pace throughout the event and will start last.
"Akiyoshi san has struggled today which has been a surprise to us and to him," said Denning. "Everything we can do to help him find his normal level overnight we will certainly do. We hope he can find enough so that he will be challenging for some points in the race."
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