Words ending with -er (meaning “one who does this,” also known as an agent noun) are very old words, most dating back to Old English. In rough terms, they might be 1,000 years old or more. Agent nouns ending in -ist crept into English at the time of the Renaissance, when the study of classical languages resurged.
Agent nouns for players of musical instruments can be very old, although many of them are relatively new. Drummer, piper, and fiddler are old. Guitarist, pianist, saxophonist and harpist are not quite as old.
Here are some dates, according to Etymonline.com:
piper: Old English
fiddler: late 1200s
Drummer: 1570s
harpist: 1610s
Guitarist: 1770
pianist: 1822
saxophonist: 1851 or later
You can imagine that when new musical instruments are invented or introduced from other cultures, new names have to be invented for the people who toot, strum, or bang on them. In theory, you could apply either -er or -ist. But it’s likely that the -ist version would sound more prestigious and for that reason would just naturally catch on.
Finally, you have the problem of pronunciation. You could try to call yourself a “guitarer,” but you’d trip up your own tongue in the process. That leaf of the language-evolutionary tree would shrivel up fairly quickly.