Jaco van Gass secured gold ahead of ParalympicsGB team-mate Fin Graham in the men's C3 3000m individual pursuit final at the Izu Velodrome.
The 35-year-old Afghanistan veteran crossed the finish line a little over a second quicker than Graham, who claimed silver to make it a one-two finish.
Both riders were taking part in their first Paralympics and it was Graham who led in the early stages of the final, before van Gass took the lead and claimed top spot by 1.013 seconds in an overall time of 3.20.987.
In the bronze medal race, Australia's David Nicholas completed the podium places in a time of 3.25.877, edging out Spain's Eduardo Santas Asensio by just under two seconds.
Great Britain were guaranteed a first and second-place finishes following a blistering qualification heat from van Gass who came home in an unprecedented time of 3.17.593.
Graham had earlier finished second-fastest in C3 qualifying in a time of 3.19.780, which was momentarily a world record in its own right.
Elsewhere, there was further success on the track for Great Britain's riders, after Aileen McGlynn and pilot Helen Scott won the silver medal in the women's B 1000m time trial.
Jody Cundy also secured a silver in the men's C4-5 1000m time trial - setting a new Paralympic record in the process - to become the first man in ParalympicsGB history to medal at seven Games.