"That was the worst display I have seen from a referee for a long time," he fumed.
"With an FA Cup final just around the corner I know it is difficult for my players, they don't want to get hurt.
"But they have a right to be protected and that did not happen today.
"I am disappointed with my players. They have got to be stronger and not be bullied out of the game.
"But we weren't out-muscled, we were out-kicked."
Jones was particularly incensed at the penalty decision which cost his side victory after a challenge from centre-back Glenn Loovens which halted a surging 70-yard run into the box by Scunthorpe full-back Marcus Williams.
"The referee was putting the whistle to his mouth even before the challenge had been made," insisted Jones.
Scunthorpe boss Nigel Adkins was happy to get the last minute bonus of a penalty kick.
"In the first half we hardly put in a tackle at all," he insisted.
"We sat them down at the interval and did not mix our words.
"I was much happier with our second-half performance.
"We may have just been relegated but we are not going to roll over.
"All season my team have played with plenty of pride and plenty of passion and that's what we produced in the second half.
"After all the decisions that have gone against us this season it makes a pleasant change when we get a late penalty to help us win the game."