The Tosfos Rid in Bava Kama (116a) says that Rebbi in fact was praising the words of Rebbi Yosi because they were reportedly stated in the name of Chagai etc., but not saying that he unequivocally rules like him. Indeed, the Rambam (Hilchos Bikurim 10:13), Tur (Y.D. 333), and others rule like Beis Hillel.

(However, it should be noted that the Rif indeed rules like Rebbi Yosi. The Yam Shel Shlomo toowonders how it is possible for the Poskim to ignore the fact that Rebbi rules this way, and that it is essentially a ruling of the Nevi'im.)

All the best,

Yaakov Montrose