The answer is: You can't.
But you can trick Blender to do so:
Let's say we have two triangle faces in random locations. They are part of one object:
What we can do to align the faces is this:
1) Since we cannot automatically align the faces in edit mode, we will select one face, and P to separate it into another object, and transform origin to geometry:
2) Align the two objects by selecting both, going to object > Transform > Align, and SHFT-RMB on all axes. This is the result:
Now the objects are aligned so that they are only visible as "one" object.
If you want to connect the faces when making one object, follow these next steps. If not, then skip to step 4.
3) Select one, move it down to about the bottom of the other, (try to make exact as possible), and rotate the object so that is perpendicular to the former like this:
4) Select both objects, and press CTRL+J to join to one object.
(optional) 5) Join the faces on one edge. Origin to geometry first, then go to edit mode. Choose select edges and select the edges where the triangles meet.
Now press F to mark as a face. This is the final result when one face is moved:
The faces are aligned and joined.
I hope this solved your problem.
Note: Please don't mess up the location of the faces, and if you do, Don't Worry!
Just press CTRL+Z, and you're fixed.