I think using these built-in functions will help:
1. handle01 = plot([X1,X2],[Y1,Y2],'.','MarkerSize',10);% draw two points to represent two balls.
2. handle01.XData = [newX1,newX2];handle02.YData = [newY1,newY2];drawnow;% update the location
and you could plot the collision more beautiful with a little more input arguments according the matlab manual.
here is a pseudo-code:
handle01 = plot([x1,x2],[y1,y2],'.','MarkerSize',10);
for ind1 = 1:maxIteration
[x1,y1,x2,y2] = yourGoverningEquation(...
handle01.XData = [x1,x2];
handle02.YData = [y1,y2];