Shanks dominated the gold medal ride in the 3000m event to beat Britain's 2008 Olympic silver medallist Wendy Houvenaghel in a repeat of their final at the Commonwealth Games in New Delhi two months ago.
It follows the gold medal anchored by Shanks in yesterday's final of the women's team pursuit.
"I have to be happy with that. I had a big break after the Commonwealth Games and have only just kick-started the season again in the last month," Shanks said.
"To be brutally honest I really wanted to crack that 3:30 mark tonight. I have ridden 3:30 so many times and only been able to crack that into the 20s to win the world champs back in 2009.
"I thought given the conditions tonight I was hoping to break that 3:30 barrier but there's plenty to work on and I have just started my season."
Shanks went close to her best with a time of three minutes 30.868 seconds in the qualifying ride with Houvenaghel second on 3min 32.226sec on a slick track.
The New Zealander showed the benefit of a solid build-up when she went faster at 3min 30.258sec in the final, finishing in the same straight as the Briton.
Palmerston North's Simon Van Velthooven finished fifth in the final of the keirin.
He missed out on automatic qualifying, but won his repechage and semifinal to give him high hopes going into the final.
However, he had to bow to a high class field in which six-time world sprint champion Gregory Bauge, of France, did not even make the final.
Meanwhile, 21-year-old Timaru rider Shane Archbold finished eighth overall in the men's omnium, the six-discipline event which has been included in the 2012 Olympics for the first time.
In a significantly stronger field than when he won in the Melbourne World Cup, Archbold was fifth today in the individual pursuit, 12th in the scratch race and seventh in the 1000m time trial to be.
He is now third overall in the World Cup standings.
Selected results:-
Women's 3000m individual pursuit, qualifying: Alison Shanks (NZ) 3:30.868 1, Wendy Houvenaghel (Britain) 3:32.226 2, Pascale Schnider (Switzerland) 3:40.054 3, Caroline Ryan (Ireland) 3:40.600 4. Gold medal ride: Shanks 3:30.258 1, Houvenaghel 3:32.226 2. Bronze ride: Schnider 3:38.403 3, Ryan 3:39.314 4.
Men's omnium
4000m individual pursuit: Juan Arango Carvajal (Colombia) 4:25.092 1, Ed Clancy (Britain) 4:26.708 2, Eloy Rovira (Spain) 4:26.999 3. Also: Shane Archbold (NZ) 4:32.971 5.
15km scratch: Artur Ershov (Russia) 1, Zach Bell (Canada) 2, Niki Byrgesen (Denmark) 3. Also: Archbold 12.
1000m time trial: Clancy 1:01.773 1, Carvajal 1:02.007 2, Martyn Irvine (Ireland) 1:03.533, 3. Also: Archbold 1:04.635 7.
Overall after six events: Clancy 24 points 1, Carvajal 26 points 2, Bell 37 3. Also: Archbold 54 8.
Women's omnium
250m flying lap: Sarah Hammer (US) 14.384sec 1, Jollen D'Hoore (Belgium) 14.576 2, Tara Whitten (Canada) 14.608 3. Also: Joanne Kiesanowski (NZ) 15.091 12.
Points: Hammer 45 1, Jamilla Machacova (Czech Republic) 28 2, Charlotte Becker (Germany) 27 3. Also: Kiesanowski 2 14.
Elimination: Hammer 1, Pascale Jeuland (France) 2, D'Hoore 3. Also: Kiesanowski 4.
Standings after three events: Hammer 3 points 1, D'Hoore 12 2, Whitten 13 3. Also: Kiesanowski 30 8.
Men's keirin, round one, heat two: Gregory Bauge (France) 1, Simon Van Velthooven (NZ) 2, Mjlsane Phillip (Trinidad and Tobago) 3. Repechage, heat five: Van Velthooven 1, Hersony Canelon (Venezuela) 2, Peter Lewis (Australia) 3. Semifinal one: Van Velthooven 1, Fablan Puerta Zapata (Colombia) 2, Francois Pervis (France) 3. Semifinal two: Aziz Awang (Malaysia) 1, Denis Spicka (Czech Republic) 2, Jason Kenny (Britain) 3. Final: Awang 1, Pervis 2, Spicka 3. Also: Van Velthooven 5.
