The Blues slipped to their sixth straight defeat courtesy of goals from Jeff Hughes after 81 minutes and Francois Zoko three minutes from time.
But the administration-ravaged club battled hard and showed solid organisation for a team assembled from loanees and players on one-month contracts.
Whittingham gave the likes of Dan Butler and Jed Wallace their first League One starts against Hartlepool on Saturday and kept them in his starting line-up.
The Pompey chief is determined to give the club's youngsters vital experience in their uphill struggle against relegation.
He said: "It's great for them and it's good that they get to taste first-team football probably a lot earlier than they would have done if the club was running normally.
"That's a big advantage for them and they have to take advantage of that. They need to realise they're in a League One club and they are now that type of player.
"They have to step up to the mark and make sure they're good enough to play week in and week out because it's a cruel world out there.
"It's a shame when people work so hard and don't get anything for it. So those guys need to toughen up and shape up, bounce back for the next one, go out and do their best again."