Brighton were clearly the better side against Newcastle when Will Hoskins, signed from Bristol Rovers in 2011, netted the second goal late on to seal the win after Andrea Orlandi had put the Seagulls ahead before the break.
The Magpies were without injured Papiss Cisse in a week which saw strike partner Demba Ba sold to Chelsea, hopes to have players back against Norwich next weekend.
Pardew added on ITV1: "We are missing too many of our top players.
"The season we're having we just need to get our best players back.
"We need to sustain ourselves in that and make sure we are a Premier League team next season.
"That team (against Brighton) is a shadow of the team we can put out."
Pardew hinted he might move in the transfer window to strengthen his injury-hit squad.
He said: "We know we need to get some bigger players who can handle the situation of carrying a Newcastle jersey, whether that's a signing or getting a player back from injury."
Brighton manager Gus Poyet paid tribute to his players.
"They realised the opportunity and we were lucky that Newcastle couldn't bring their best players," Poyet said.
"We didn't create too many chances today but we were a good team to play against a Premier League team."
Hoskins believes the FA Cup giantkilling against Newcastle reflects the ambition shown by the npower Championship side.
Hoskins told ITV1: "We did what we set out to do, play our way and not get fazed. It's a good result for us.
"This is why I signed here, great ambition and the club's fantastic."
Orlandi's opener was well taken with a deft touch putting his side a goal ahead.
Orlandi said: "It was a really nice goal, I was pleased with that.
"I don't know how I did it to be fair but it was a nice goal.
"We all played really well. It's great for us."