No, you're thinking of Mark Waid's Birthright from 2003. It was John Byrne's 1986 reboot that established Jonathan and Martha Kent as being alive and well in Superman's adult life, in contrast to the pre-Crisis continuity in which they'd both died while he was still Superboy living in Smallville. That's been the official DC Universe continuity ever since, although Birthright tweaked various elements of it (and some of those tweaks were later retconned out of existence in one of the reality-remaking "Crisis" miniseries).
Christopher has got this exactly right.
As far as I know, the only versions of Superman in which Jonathan Kent has died while Martha has lived on have been the feature film series, Smallville, and the 2007 Superman: Doomsday DVD animated feature. In everything prior to 1978, both Kents died before Clark went to Metropolis. In everything else post-1986, to the best of my knowledge, both Kents continued to be part of Clark/Superman's life in the present day. (See the 1988 Ruby-Spears animated series, Lois & Clark, and the DC Animated Universe as well as the comics.)
You left out one, I think: in the first episode of the George Reeves series, "Superman on Earth," Pa Kent dies, leaving an adult Clark to bid goodbye to his still-living Ma (interestingly, their names were "Eben" and "Sarah" at that time, not "Jonathan" and "Martha," IIRC, these names came from George Lowther's prose Superman novel of the Forties).
What they don't tell you is that in Action Comics #871, Superman turns back the world and doesn't allow this to happen.
No, actually, Superman and Lois will make a deal with Neron to sacrifice their marriage in order to save Pa Kent's life. This will make things "better."
