The result was delayed after the British team lodged a protest over the role played by a marshal on a jet ski in correcting Beaugrand’s direction during the swim.
Potter could have claimed a second world title had her French rival been disqualified, but had to settle for second place overall after the protest was rejected.
The 32-year-old Briton, who won Olympic bronze at this summer’s Paris Games, made a late lead to move into silver medal position and ultimately finished 12 seconds ahead of France’s Lombardy, who was third overall.
Fourth-ranked Holland, 38, who won the world title in 2018, recently returned to the sport after taking time off after the birth of her first child.
“I always said I wanted to get back to the level I was at before I had my baby, which was roughly in the top 10,” she said after finishing fourth on a strong race.
“So I’m absolutely happy with it, it’s better than I thought. Back with the big girls for the last time. I’m so happy to do it.”
Britain’s Olivia Mathias finished 14th, 2 minutes, 47 seconds behind winner Beaugrand, with her teammate Jessica Fullagar 16th, Kate Waugh 19th and 2020 world champion Georgia Taylor-Brown 21st.
The BBC will have full coverage of the elite men’s race on Sunday, October 20.