I think you're thinking of CommonMark. That link format isn't valid in canonical Markdown either (just to some of the common variants that also went by "Markdown").
I was always partial to the variants that could do citations well. They would automatically link-ify items postfixed by [1] etc with the link included at the citation at the bottom. I implemented a customer facig newsletter system at one job using that, where it automatically made the emails multipart when markdown was submitted, with the text part being raw Markdown. When using citations, it's still very readable.
I thought CommonMark was the attempt to standardize Markdown. Besides that, every markdown implementation I've touched since before CommonMark supported [text](url) format.
Actually, I'm totally wrong. I thought this wasn't part of the original spec for some reason, but it's totally in Gruber's list of features and works in Markdown.pl, I just missed it when checking to confirm originally (I saw automatic links and missed the other links feature).
Thanks for causing me to look again (I used babelmark[1] to check what versions supported it and noticed all of them do, including Markdown.pl). I dislike putting out wrong information. :/