This is a tricky one.
1) (required) unlock the move under the stats page. Under the Defense tab, the top left one called Punishing Counter. Get that to 2/2. Notice that it says you NEED TPKO to be at the threshold.
2) (optional, but super helpful) reduce Raph's TPKO from 10 to 5. Under the Combat tab, go to the bottom and get TPKO Threshold to 2/2 so you only need 5 instead of 10 combo.
3) Go to the dojo and get the hang of it. Build up to TPKO how you want, and keep it ready. Then when the dummy attacks, hit B to counter and RIGHT after press and hold RT + X. Raph will put them on his shoulder, then drop them to the ground, then climb around and perform a submission, like yank on their arm. That's the move you are looking for.
(vid1 - dojo)
4) Go into a challenge mode, like Alley, and then start racking them up. Near the points/exp counter you will see "Submission TPKO" when you do it right.
(vid2 - challenge mode)