Once a payment is scheduled and the extension was accepted, you will have to call the IRS's payment services hotline to cancel any automatic payment you have scheduled. They advise to wait 7-10 days after your return was accepted before calling to give the system time to reflect your information.
If you have any issues using the above number, you can also call the regular IRS number at 800.829.1040 to speak to a regular customer service representative.