Trott, who won team pursuit gold on Saturday, successfully defended the title she won at London 2012 to take her to four career Olympic gold medals, the most for a female British Olympian.
The Briton finished with 230 points, 24 clear of her nearest rival, after enhancing her advantage in the discipline which was once her Achilles heel.
Sarah Hammer, of the United States, was second on 206 points and Belgium’s Jolien d’Hoore third on 199.
Trott won three of the first five disciplines to move on to 196 points entering the points race, which took place over 100 laps and featured 10 sprints. Trott won the fifth sprint – and the sixth – to move 31 points clear, but with 12 laps to go, d’Hoore and Hammer attacked again. But the Briton again reacted, reeling them in, before crossing the line victorious.
A fourth gold saw Trott move above Charlotte Dujardin after the equestrian rider won her third gold on Monday.
Meanwhile, Becky James claimed her second silver medal of the Games in the women’s sprint and Katy Marchant claimed bronze in the race for third.
Multiple world champion Kristina Vogel of Germany won gold.