Yes, "to make a call" does also mean "to make a decision." The reason that you may have heard it less often stems primarily from the fact that "to make a call" has a different nuance than "to make a decision."
"To make a decision" usually requires some deliberation, weighing benefits against harm. On the other hand, "to make a call" has the additional nuance that you are faced between two almost equally attractive (or unattractive) choices, and you *must* choose one over the other. In other words, "to make a call" gives the hearer the impression that the decision was, well, "a close call."
That is why you usually hear "to make a call" in sports, when an umpire has to decide whether there was a foul when perhaps the line between "foul" and "no foul" is actually quite blurry...
Hope this helps.