Can I call a phone number from the Terminal?

You can with open "tel://+316123456789" start a phone call process - but you still need to click on the "Call" button to make the call.

To do so, you may also simply press ↩. To automate everything via Applescript:

open location "tel://+351918306031"
delay 2
tell application "System Events" to key code 36

In theory, you could use Automator to setup a sequence of actions to trigger making a call. I've never actually used Automator, but my understanding of it says it'll work.

First, you could create an Automator script that perhaps triggers Rene's answer of running open "tel://+316123456789" and clicking the 'Call' button. Or, you could have it open the Google Hangouts Chrome Extension and similarly dial a number.

Second, you would call the Automator script from the command line (as described here):

open MyAutomatorCaller.app --args '+316123456789'

Lastly, you could create a Bash alias for the above command (i.e. in ~/.bash_profile):

call() { 
    open MyAutomatorCaller.app --args $1
}