It was feared the penalty, incurred after Pompey finally came out of administration, would be carried over to next term.
But Portsmouth, who had already been condemned to relegation, merely slipped from 22nd to the foot of League One.
The decision means the club, now under the ownership of the Pompey Supporters' Trust, will kick off in League Two next season on a level playing field.
Whittingham said: "It's what we were all hoping for.
"We want to start next season on an even keel because it gives you a chance."