Pearce was involved in the previous match, against Spain at Pride Park, as the Under-21 team prepare for this summer's European Championships in Holland.
The City boss was capped 78 times by England - and Pearson said he sympathised with Pearce over the fact that the Manchester City boss would not be leading the team out ahead of Saturday's historic match, which will be played in front of 60,000 fans.
"It is something we just have to deal with, though I feel for Stuart personally," said Newcastle assistant boss Pearson.
"It's nice for me but in an ideal world it would be nice for Stuart to be there.
"He'll be at the game like he would be anyway but he won't be in the dressing room."
I don't think it will take any time at all for Wembley to grab the imagination of players and coaches
Pearson, along with fellow coach Steve Wigley, took the Under-21 team through a training session at an overcast Wembley on Thursday.
The team looked relaxed and enthused to be inside the new stadium - and Pearson said it was noticeable how excited the squad were to be involved in the Saturday's fixture.
"This is the beauty of occasions like this," said the 43-year-old.
"Speaking to the players, this is a major thing for them. It's fantastic for English football to be back at home and they are very lucky people to be playing there.
"It is vitally important for us that the national stadium is up and running.
"Wembley is the home of English football - to go out there was a great feeling.
"I don't think it will take any time at all to grab the imagination of players and coaches, and for fans as well it will be a fantastic stadium to come to watch games."
Pearson was skipper of the Sheffield Wednesday team that won the 1991 League Cup final.
The second division Owls, managed by Ron Atkinson, defeated Manchester United 1-0 and central defender Pearson - up against Mark Hughes and Brian McClair was Man of the Match.
"Unfortunately it was the only time I was on the winning side in a cup final," he added.
"It's a very fond memory still, I'd be lying if I said I never thought about it. I'm not a player any more, I'm a coach and you move on, but those memories stay on with you forever."
But despite the historic nature of the occasion on Saturday - and the resonance of past glories that playing at Wembley brings to mind - Pearson was keen to place the match in context.
The European Under-21 Championships take place in June - and England are in the same group as Saturday's opponents Italy.
"Although Saturday's is a big game and a showcase event, in the bigger picture it is a build-up game," said Pearson.
"It will be a tough game and one they need to be focused on.
"It is important that everyone enjoys the occasion but keeps in mind the tournament in the summer."
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