If you look carefully at the Gemara it doesn't really say that.

> א"ר יוחנן בלולה במקרא בלולה במשנה בלולה בתלמוד (איכה ג, ו) במחשכים הושיבני כמתי עולם אמר ר' ירמיה זה תלמודה של בבל

R. Yochanan is talking about Babylon, or more specifically the Torah scholars there. There doesn't seem to be an indication that he is referring to the Babylonian Talmud. R. Yirmiah, on the other hand, applies R. Yochanan's teaching to the Babylonian Talmud (though even in his day it wasn't a finished product).