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."
Notts County boss Keith Curle paid tribute to stand-in goalkeeper Fabian Spiess as the Magpies ground out a hard-fought three points.
He said: "The most pleasing thing was Fabian. I just call him Fab. He put in an assured performance, showed good handling, correct decision-making, he was coming for crosses and dealing with things.
"Our back four were comfortable with him behind them and that's the most pleasing thing for me. He got his first professional clean sheet so early in his career."
- Sports & Recreation