Since when

Can shadow jago do his ultimate as a normal attack… I just fought someone online who did it to me twice in a row when he had no health left to win the match

Always. You can do it when you activate his instinct. But once you do it, your instinct is over. The more instinct you have left when you do it, the more damage it does.

Since the day he was released after his new moveset was created.

Please change the clickbait-y title.

It sounds like he used his Annihilation special move (using Instinct), then finished you with his Ultimate.

A replay would help to clear this up, if you can share one.