I would guess that some of the champions back in the old days, when the top category (in double jeopardy) was only $200, made less than any champion once they increased the amounts tenfold.
According to wikipedia, both Benjamin Salisbury and Brandi Chastain won Celebrity Jeopardy! games with the smallest amount possible, $1.00. Since Celebrity Jeopardy! champions do not return the next day, they would never have had an opportunity to win more.
Since the celebrities are playing for charity, the show probably gave them more than that. As I recall, the winner of each celebrity game gets some minimum amount for their charity regardless of what their final total is.
There has been a “regular” game - in fact, the second episode with Trebek as host - where all three contestants ended with zero; however, the defending champion won a few thousand dollars on the first show.
Suggestion: we can search the Jeopardy Archive for one-time champions and see who had the smallest win. However, it’s incomplete before 1997 or so. The smallest I have found so far: Yolanda Diaz, who was a one-time champion in Season 14 with $2000 (plus whatever consolation prize she won in her second game).