Shanks produced a time of 3:30.199 at Melbourne's Hisense Arena to comfortably beat Houvenaghel on 3:32.350.
The 2009 world champion rode a personal best 3:27.268 in qualifying.
Shanks beat Houvenaghel to win her world title in 2009 but Houvenaghel beat the Kiwi in the semifinal at the worlds the following year.
Shanks got the better the pair in the gold medal ride at the Commonwealth Games later in 2010.