Text substitution does not work with Slack on Yosemite
Even after following the instructions in the accepted answer, this still did not work for me until I followed these instructions. Basically, run the following in a terminal:

defaults write -g WebAutomaticTextReplacementEnabled -bool true

or to only change Slack's behavior (and not pollute your global domain):

defaults write com.tinyspeck.slackmacgap WebAutomaticTextReplacementEnabled -bool true