Just one method to convert 2D to 3D geometry with shapely

shapely2D_to_3D.py

# -*- coding: utf-8 -*-
from shapely.geometry import LineString
from shapely import wkt

line = LineString([(0, 0, 5), (1, 1, 5)])

# memo for 3D
wkt3D = line.wkt

# 2D
wkt2D = line.to_wkt()

geometry2D = wkt.loads(wkt2D)
print geometry2D.wkt

I think a better approach is to use shapely.ops.transform.

import shapely.ops

p = Point(2, 3) # no z
pz = shapely.ops.transform(lambda x, y: (x, y, 2), p) # now pz is p with a z coordinate

This can also be used to convert other geometries. And the other way around, to remove the third coordinate:

l = shapely.geometry.LineString(([2, 3, 6], [4, 5, -1]))
shapely.ops.transform(lambda x, y, z=None: (x, y), l).wkt  # 'LINESTRING (2 3, 4 5)'