plot3(x,y,z) will produce 1 line object for each column of the inputs. Each line object can have its own color. So, all you have to do is arrange the data properly.
h = plot3([x(:).'.*[1;1]], [y(:).'.*[1;1]]), [z1(:).', z2(:).'], '-');
set(h, {'Color'}, mat2cell(jet(numel(x)),ones(numel(x),1),3));
The syntax [x(:).'.*[1;1]] produces two rows of identical x values.
The mat2cell() syntax converts your color matrix to cell array of 1x3 values.
