Two points:
1) Realise that Superman #61 1949 by Bill Finger and Al Plastino is the first actual story linking Superman to Krypton (thanks for that reference). My comment was about when SuperBOY first met Jor-El. [Not even sure if my quoted reference is the story I am thinking of.]
In terms of Superman actually meeting Jor-El, though, I sort of assume that "Superman's Return to Krypton" (1960) is their only real canonical encounter. It was referred to again in an issue of World of Krypton, in which the events are seen from Jor-El's point of view.
2) Of course, the point raised by Permanus is valid and I suppose gets to the crux of the matter of what is regarded as canonical and what isn't. As far as I recall, the meeting of Superboy with Jor-El (as a boy) does not contradict "Superman's Return to Krypton" (as this is written fro Jor-El's perspective)? In the story I am thinking of, there was a neat twist in where Superboy gives (the boy) Jor-El a box which turned out to contain Red_K (as evidence of Krypton's fate?) that had the effect of blanking Jor-El's memory.
Jimmy