"It cuts you deep. Being Olympic year and with it not being there, it hurts a bit."
Still, she now has a second coveted rainbow jersey to frame and hang on the wall.
Shanks took control of the final against Great Britain's Wendy Houvenaghel from the start, establishing more than half a second lead at the first of three kilometres.
She extended that lead to 1.390s at the 2000m and there was no coming back for the Brit.
Shanks' winning time was 3m 30.199s.
"It's a great feeling," Shanks said. "I've been world champion once before and it's so hard to get. Once you have that feeling it makes you want it even more.
"My form in the team pursuit has been good. All the data shows I've got great form, but it was a matter of putting it out there.
"I haven't been focusing on the individual so it was a bit of the unknown, but my legs felt great today," said Shanks, who is coached by Dayle Cheatley.
Australian Ashlee Ankudinoff won bronze, beating compatriot Amy Cure by 0.049s.
Shanks' win ensured New Zealand would claim their largest haul of medals at a world championship, surpassing the four they won in Apeldoorn last year and at Copenhagen in 2010.
It will not, however, translate into a similar haul at the Olympics.
The pursuit medals won by Shanks and Westley Gough are both in non-Olympic disciplines.
As admirable as the team sprint was in claiming bronze, they cannot rely on the luck that saw two of the favoured teams - Germany and Great Britain - disqualified.
That leaves the men's team pursuit and the keirin as the best chances for medals.
Others, including the women's team pursuit, are hoping they can make the improvements needed to force their way into contention four months from now.
Shanks admitted that the individual pursuit had become a secondary focus as she instead focused on honing her combination with Lauren Ellis and Jaime Nielsen in the team pursuit.
But last night was all about her.
She scorched into the gold medal ride with a 3km ride of 3m 27.268s, taking 1.207s out of her previous personal best.
"I had to make a PB [personal best] just to make the final," Shanks exclaimed.
Adding to the sense of occasion was the fact that she was riding off against one of her best friends, Houvenaghel. They have been duelling in earnest since 2009, when Shanks beat her to win the world title in Poland.
"We've had a few battles and last time we raced on this track she beat me by 0.2s.
"I tend to back up pretty well," Shanks said, "and I was confident that if I went out there and executed my plan in the first half of the race I would be able to push it and race her home."
Both were assisted this week by the absence of the defending world champion, American Sarah Hammer, from the field. She instead focused on the Olympic-discipline omnium.
That will not matter to Shanks as she now contemplates how she can help eke more time out of the team pursuit that finished fourth behind Great Britain, Australia and Canada on the boards at the Hisense Arena.
Shanks said this week that for New Zealand to claim a medal in that event at London, all three were going to have to start pulling even laps.
In that regard she's laid down a formidable marker to her teammates. Nielsen finished 10th in 3m 35.286s and Ellis a further 2.639s back in 12th.
