The Eagles boss was furious at the official's failure to award a penalty early in the second half for Tommy Miller's foul on Nick Carle, when Palace were 2-1 behind.
Warnock was so incensed he brought one of his backroom staff to his post-match press conference to show journalists video footage of the incident, which he claimed should also have produced a red card for Miller.
Warnock blamed Penton's fitness levels for his failure to give the spot-kick.
He said: "I'm disappointed. It was a major decision in the context of the game and he hasn't given it.
"Miller got nowhere near the ball and it's criminal, the decisions we're not getting at the moment. How the hell can't you see things like that?
"I think experienced referees should stay on but if Clive's not fit enough to keep up with play there, that's not on.
"That's not my fault, that's down to his fitness. I know it's his last year [as a Football League referee] but he has to be better than that.
"Games are changed by things like that. If it had happened at 3-1 or 4-1, then you wouldn't get any complaints. But 2-1? Dear me.
"I don't think we should have video evidence for penalties - I just think a referee should be able to see an incident like that and make the right decision."
Warnock had a case for the penalty, but Palace were themselves fortunate to see their goal - which halved the deficit after Owen Garvan and David Norris had fired Ipswich 2-0 ahead after 28 minutes - stand.
Julian Speroni launched a free-kick downfield and Alan Lee rose highest to send a glancing header into the bottom corner.
The linesman raised his flag immediately, believing offside defender Jose Fonte had helped in Lee's effort, but Penton overturned the decision after a lengthy consultation.
Ipswich made the most of their good fortune after Miller's escape to seal an impressive win with a strike from substitute Kevin Lisbie and Clint Hill's last-gasp own goal.
Now boss Jim Magilton wants his side to show the consistency required to mount a concerted push for promotion.
He said: "Hopefully we can be in the promotion shake-up. There's a bit of a gap developing but all the teams can beat other and that hasn't changed.
"We've beaten Reading at home but we need more consistency. I just hope we're making our move at the right time. It's a marathon not a sprint.
"We knew we had to come here and compete. The scoreline probably flattered us but we showed great togetherness, character and grit.
"It's one Saturday gone and hopefully we can build some momentum from here."