This happened, in Turtle Soup, penned by the Turtles founders.. They had them about even, with Usagi looking a tad better, but Leo winning because Usagi made a mistake and took a fall.
This was a much younger, less experienced Usagi, so its likely that thanks to being in a world of very good swordsmen and dueling on a regular basis, he improves to the point of besting Leonardo, who doesn't get the same opportunities to practice his skills against a wide range of competition.
A little something I found about The Rabbit Bodyguard, Miyamoto Usagi:
He is one of the better swordsmen in Japan. Stan Sakai says "Usagi is not the best swordsman around. He had lost to Nakamura Koji, who, himself, was defeated by Katsuichi. However, Usagi is better than most. Also, his ‘unusual style’ gives him an advantage." Sakai also states "Usagi is nowhere near the best swordsman in Japan. He was beaten by Koji, and wounded by Jei. He has not been tested against many others including Katsuichi and the Lord of Owls. So far, the best of the swordsmen I've introduced is Inazuma." Of course, one must realize that out of the hundreds (if not thousands) of samurai, ronin, and bandits around, Usagi has been wounded or beaten by (or apparently isn't as good as ) maybe five people (Inazuma, Jei, Katsuichi, Nakamura Koji, and Zato-Ino). Sakai has also made it clear that the comments about Zato-Ino being the best swordsman were made before he developed and introduced the character of Inazuma.
What makes Usagi so good? His speed is one. He is very fast, both with the blade and on his feet, several times performing Multiple-Move Bys and hitting upwards of around a dozen people. He also uses his Sweeping Strike to great effect, cutting down droves of bandits and lesser swordsmen in many panels. He's also very alert, had to surprise, and hard to put down. He may not be the best swordsman in the world of Usagi Yojimbo but I'd put my money on him anytime he gets into a sword duel. And even if he loses, his foe is not going to have an easy time of it.
From Sakai's words , it seems the best Warrior ranking of UY universe goes like this:
1. Inazuma
2. Zato-Ino
3. Katsuichi
4. Nakamura Koji
5. Jei
6. Miyamoto Usagi
Not considering some characters that can tie with Usagi. Those top 5 are better than the Rabbit Ronin. But Usagi can give 2-5 a good fight even could beat them.
Wonder where would Master Splinter and his turtles rank in this mix.