I've never done 3D plotting before, so I can't say whether this would be the best method using the tools matplotlib
has to offer. But you could make good use of the zip
function.
pos1 = np.array([[0,0,0],[2,2,2]])
pos2 = np.array([[1,1,1],[3,3,3]])
for point_pairs in zip(pos1, pos2):
xs, ys, zs = zip(*point_pairs)
ax.plot(xs, ys, zs)