Olympic and five-time individual sprint champion Lavreysen has been almost unbeatable in the discipline but suffered a rare loss as Richardson edged him in the final at a packed London Velodrome - Lavreysen showing his frustration on the line.
The 26-year-old responded, though, to win a thrilling keirin final after the British-born Richardson launched an audacious early attack but could not hold off a storming Lavreysen.
Richardson will make his Olympic debut next year and looks the biggest threat to Lavreysen's domination, although the Dutchman is clearly up for the fight.
"I think it's a big thing," Lavreysen said of his growing rivalry with Richardson after wrapping up the overall sprint title after the five rounds of the Champions League in which he won seven of the 10 sprint and keirin events.
"I think it's a good thing for the sport. It keeps me fresh because I really need to be focused and every time I see him in the track I know I need to make maximum effort.
"He tried to stick it to me in the keirin final. We are at the Olympics next year, and that's not going to happen."
While Lavreysen won back the overall men's sprint title he won in the inaugural Track Champions League in 2021, Britain's Katie Archibald also reclaimed the women's endurance title.
Shed was eclipsed by team-mate Neah Evans in the 20-lap scratch race and was disappointed not to make it five wins out of five in the elimination race where she came third.
But her consistency throughout the rounds in Mallorca, Berlin, Paris and London made her a worthy champion and will send her into an Olympic year full of confidence.
"It's a shame not to win the final races as this is the night my sister came to watch, but I'm really happy to win the overall title again," the two-time Olympic champion said.
Canada's Dylan Bibic did enough on the final night to wrap up the men's endurance title while New Zealand's Ellesse Andrews crowned her women's sprint title in style, winning both the sprint and the keirin in impressive fashion.
Each title winner is awarded prize money of 25,000 euros each.