Taylor-Brown, who trains at the Leeds Triathlon Centre, went into the race as the reigning world champion and one of the favourites for the title but had to play catch-up on the 10 kilometres run after getting a flat tyre on the last lap of the bike leg.
She quickly caught team-mate Jess Learmonth, who finished ninth, and Germany’s Laura Lindemann and then reeled in American Katie Zaferes to match fellow debutant Alex Yee’s achievement in the men’s race and win Britain’s seventh triathlon medal in the last three Games.
But there was no catching Duffy as the the 33-year-old, who was awarded an OBE in 2018, showed herself to be the class of the field with a historic victory for Bermuda, whose only previous Olympic medal was a bronze for boxer Clarence Hill in Montreal in 1976.
Learmonth split the field from the start with a blistering 1.5km swim, establishing a lead group that dwindled from seven to five but never looked like being caught.
Tropical storm Nepartak had been threatening the coast of Japan for several days and Tuesday morning brought wind and heavy rain.
The start was delayed by 15 minutes to allow athletes extra time to prepare, but when they did get under way – this time thankfully with no interference from boats – Learmonth’s intention was clear.
The Leeds athlete went straight to the front of the pack and set a fearsome pace. The field was soon strung out across Tokyo Bay and by the end of two laps seven women had a gap of more than 30 seconds.
Those seven contained several of the medal favourites, and on the third lap the seven became six when American Summer Rappaport dropped off the pace.
The leaders maintained an advantage of more than a minute, while behind them several athletes came off their bikes in the treacherous conditions.
Brazilian Vittoria Lopes lost touch with the lead group on lap six and the only blessing for Taylor-Brown was that her puncture came with only a few hundred metres to go.
She started the 10 kilometres run 22 seconds down, with Duffy and Zaferes already up the road, but Taylor-Brown is a talented runner and she soon overtook Learmonth and Lindemann to climb into the medal places.
The 27-year-old from Manchester was tantalisingly within touching distance of Zaferes for two laps but made her move just before the bell to climb into second and put her hands to her face in disbelief as she came down the finishing straight.