Apple - How to disable ellipsis autocorrect on macOS?

Go to System Preferences, select Language & Text, then the Text tab, and deselect the box for that option.

Or you can disable the feature completely by deselecting the box at the top.

In Mavericks at least, this seems to be controlled by the "Use smart quotes and dashes" feature found in System Preferences → Keyboard → Text. Uncheck the box, and the behavior goes away, even in Evernote.

If "Smart Quotes" is active in Keyboard Settings but you don't want smart ellipses, Edit menu in most applications on OS X Yosemite, unchecking "Smart Dashes" found in Edit -> Substitutions -> Show Substitutions stops autocorrect of three periods to ellipsis.