In a repeat of the all-British Rio 2016 final, Storey once more got the better of compatriot Crystal Lane-Wright.
The relentless defending champion laid down a marker earlier on day one of Tokyo 2020 by shaving more than four seconds of her own world record in qualifying, powering over the line in 3:27.057
She did not need to repeat the trick in the deciding race at the Izu Velodrome as she remarkably caught Lane-Wright inside eight laps following a rapid start, leaving her rival to settle for another silver.
In winning her country’s first gold of the Games, Storey took her total haul to 15 Paralympic golds - one short of swimmer Mike Kenny’s British record - and a phenomenal 26 medals overall.
The 43-year-old will have a chance to surpass Kenny next week when she attempts to defend her C5 time trial and C4-5 road race crowns.
“For me as an individual, I’ve won a medal at every single Games I’ve been to and this is my fourth time winning the individual pursuit in a row,” she told Channel 4.
“I broke the world record in Beijing, in London, in Rio, this morning, so for me it’s been quite overwhelming to try and keep backing that up and keep pushing on the pedals to go faster and faster.
“I never expected to go as quick as I did this morning but I’m so glad that I did.”
Due to the coronavirus pandemic, Storey arrived in Japan having not performed competitively on the track since January 2020 but in confident mood.
She was also without the support bubble of husband and fellow track cyclist Barney, eight-year-old daughter Louisa - who travelled to Rio five years ago - and three-year-old son Charlie.
Yet there were no signs of rustiness or adverse effects in the heats as a superb ride underlined her class and sent an ominous warning to her rivals.
Lane-Wright had finished more than eight seconds adrift of that record-breaking time during her initial 12 laps - a personal record of 3:35.061 - and would have needed to have pulled of a major shock to close the gap in the medal race.
It never looked likely to materialise.
Storey, whose illustrious career began as a swimmer and has now spanned eight Games, flew out of the blocks and mercilessly chased down her team-mate to secure another spot at the top of the podium and, in the process, take a major step to further cementing her place in the history books.
She waved to her family at home and was saddened they were unable to witness her latest triumph.
“Being in an empty stadium we have to be prepared to race like that, but once you finish racing that’s when it hits you, literally the stands are empty,” she said.
“Racing in a pandemic is hard. But it’s when you want to celebrate with people you realise you don’t have your friends and family here.
“We can celebrate with the team, which is obviously amazing, but there is a bigger team behind the team you see here today and now more than ever they’re missed.”
Husband Barney said: “The qualification was fairly early in the morning, at quarter to four I think in the end, so I was literally just sat watching it on my phone in bed, and then attempted to go back to sleep before the final which failed miserably.
“I got Louisa up to watch the final and both sets of grandparents have come round as well. It was brilliant just to have the usual family crew watching the event and it is just a shame we’re so many thousands of miles away.”
French rider Marie Patouillet clinched bronze after beating New Zealander Nicole Murray.
Despite never threatening gold, Lane-Wright was satisfied with her day’s work.
“As much as I’m up against Sarah, it’s me versus me all the time,” she told Channel 4.
“To get such a big PB this morning, to me that’s my gold medal. I can only control what I can do, so I am so pleased for today.
“If there’s one person that watches this and thinks, ‘I can do it’ and I inspire them, that’s more than any medal, any race I have ever done.
“Paralympic sport is still really in its infancy and it’s a hard job, but it’s the best job I’ve ever had and I absolutely love it, so please be inspired.”
Visually impaired rider Steve Bate secured GB’s third track cycling medal of the day but had to settle for silver following another irresistible performance from Dutchman Tristan Bangma.
Bangma and pilot Patrick Bos set a new world record in qualifying, becoming the first pair to go under four minutes in the event, finishing in 3:59.470.
Their stunning form continued in the final as Bate was unable to defend the title he won in Brazil after he and pilot Adam Duggleby were powerless to being caught.