No, Blender can't do this with the default feature set.
Edit: As Aldrik says, you can use pdb, however blender can't step over python code in its own interface.
There are however some things you can do that may be of interest to you.
Load as a python module
If you compile Blender as a Python module, you can use any Python IDE which supports debugging/stepping, The times I really wanted to step over Python code I did this, however it can't be used with a Blender window active.
See:
How can I run blender from command line or a python script without opening a GUI?
Use the command line REPL
REPL, being (Read–eval–print loop).
Python has a module that you can use to create a python interactive console, it can be used to execute scripts one line at a time.
See: http://docs.python.org/3/library/code.html
The example below executes 3 lines of python script, then prints a variable which the script defined:
import code
namespace = {}
console = code.InteractiveConsole(
locals=namespace,
filename="<blender_console>",
)
Code - can be anything...
load an entire text file into this for eg.
my_code = [
"a = 1",
"b = 2",
"c = a + b",
]
execute the script line by line.
for line in my_code:
console.push(line)
get something back from the executed code
print(namespace["c"])