First all, I think this result applies only if one of the balls is initially at rest, right? You can then prove the result by applying the conservation laws of energy - since it's an elastic collision - and of momentum.
Conserving energy gives you one equation in terms of the magnitudes of the three velocities (initial velocity of the one moving ball and two final velocities), and conserving momentum gives you a vector equation relating the three velocities. Combine the two equations and do a little algebra and you get the result you're looking for, i.e. the dot product of the two final velocities is zero.
And by the way, for those posters who were wondering about the collision headed directly for the center of the stationary ball, you can work out what final velocities must be in that case, and you'll see that the ball that was initially moving will be at rest and the initially stationary ball will move with the initial velocity. The dot product is still zero, so this result is consistent with the statement that the velocities are perpendicular.