Run the below command to deactivate the MFA device defined for an IAM user where username is the name of the user and arn:aws:iam::123456789123:mfa/MFADEVICE is the arn of the MFA device.
aws iam deactivate-mfa-device --user-name username --serial-number arn:aws:iam::123456789123:mfa/MFADEVICE