Commerce with foreign Nations, the Indian tribes, or among the several States. "To regulate" is to erect barriers to commerce as well as to tear them down.
"The prohibition against importation of slaves was an exception to commerce involving importation from abroad"
An exception? That very same year, "Jefferson's Embargo" cut off all trade with Europe.
In 1842, Congress forbade the importation of obscene literature or pictures from abroad. In 1848, it passed an act ''to prevent the importation of spurious and adulterated drugs''. In 1887, the importation of opium was prohibited and in 1897, Congress forbade the importation of any tea ''inferior in purity, quality, and fitness for consumption".
"If we take your analysis latterly, then there would have been no need for the 13th amendment."
The 13th freed the slaves already here.
To answer your question, the commerce clause was used early on to prohibit commerce with foreign Nations and with the Indian tribes. It wasn't until 1884 that certain commerce among the several states was prohibited.