Build and Runes
Although Master Yi cannot be slowed during his ultimate, he can still be disabled.
It’s good to pick a champion with a disable (silence/stun/knock-up/displacements) so that you can stop Master Yi from casting his Meditate.
Avoid fight him while low in health, lest he receives resets on his cooldowns for scoring a kill.
If he is doing lots of damage in short periods of time, consider getting Thornmail.