Fredriksen put in a composed performance as she touched home in a time of one minute 17 seconds, with Jessica Long from the US in second and Russia's Olesya Vladykina third.
The 26-year-old has battled ill health over the past year which has seen her hospitalised or often bed-ridden, and she came into London after just six weeks' training.
The City of Salford swimmer peeled off her cap and cried following victory.
GB poster girl Ellie Simmonds, already with two golds to her name, was in the pool immediately after Fredriksen in the final of the S6 50m freestyle and she claimed a bronze in what was one of her weaker events.
Mirjam de Koning-Peper won gold for the Netherlands.
Elsewhere Britain's Danielle Brown successfully defended her Paralympic Games title with a narrow victory over team-mate Mel Clarke in a tense women's individual compound final at the Royal Artillery Barracks which went down to the final arrow.
Yorkshirewoman Brown won Paralympic gold in 2008, the Commonwealth Games team title in Delhi two years ago and now has triumphed at London 2012.
Brown met compatriot Clarke, bronze medallist from Beijing, in the final, winning 6-4.
In equestrian, Deb Criddle claimed the silver medal in the grade 3 freestyle dressage test in Greenwich.
And in boccia, Britain's BC1/2 team landed bronze with a 7-5 win over Portugal.