Collett, Tom McEwen and Ros Canter enjoyed a perfect opening day, chalking up record low scores for the dressage phase both as a group and for Collett individually.
A total of 15.8 penalties incurred on Saturday’s cross-country stage had made it tight at the top with second-placed France, but a clear round from McEwen, with one fence down from both Canter and Collett, was good enough to seal gold.
Team GB finished on 91.30 penalties, ahead of France in second on 103.6 and Japan in third on 115.80.
Britain also triumphed in the team competition in Tokyo, with this victory making them the first nation to win the team gold medal on five occasions.
Canter was first out for Britain, knocking down the sixth fence but with the first French rider Nicolas Touzaint having had two down, Britain still held a healthy advantage.
McEwen’s clear only strengthened that position and while Collett hit the last, gold was already assured.
Collett grabs individual bronze
Collett went into the individual jumping round in third, with fellow Brit Tom McEwen 2.7 penalties behind in fourth.
Both jumped clear, but with German Michael Jung and Australian Christopher Burton also enjoying perfect rounds to take first and second respectively, Collett had to be content with third.
Collett told the BBC: “I thought (gold in) Tokyo was special but this is incomparable. It has blown that out the water. Going out in front of a crowd like this and feeling like every single person is willing you on.
“It felt like Dan felt that too. He tried so hard, I am just the lucky one that gets to steer him. I owe absolutely everything to that horse. This is just a day I will never, ever forget.”
Collett had led after the first day of competition, having scored an Olympic record of 17.5 in the dressage phase.
However, a time penalty of 0.80 for the cross-country handed the initiative to Jung ahead of the final showjumping rounds.
Collett had one fence down and a time penalty of 0.80 in the first team round, dropping her to her final position of third with a score of 23.10.
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