To plot two separate functions using the Plot3D command in Mathematica, one effective method is to create individual plot strings for each function and then combine them using the Show function. For example, to visualize the intersection of the planes defined by the equations x + y + z = 1 and x^2 + y^2 + z^2 = 1, users can define each function separately with Plot3D and then use Show to display them together. The syntax involves setting up each plot with DisplayFunction -> Identity to suppress individual displays, followed by combining them in Show. This method is applicable for both 2D and 3D plots in Mathematica.