Pardew blamed a lack of intensity.
"Forget shape, systems and so on - intensity is everything in football," he said.
"For the first two goals, we were really loose and disorganised. It was not until halftime that we got back to our level and showed discipline.
"You'd have to say we got beat by the better team."
Wigan manager Roberto Martinez hailed another fine display from his team, who have also notched wins over Arsenal and Manchester United in recent weeks.
"In every department of the club, we know we need to work really hard to keep our dream alive and that comes with belief," he said.
With Newcastle's defeat, Arsenal moved four points ahead of them to cement their grip on third place after battling to a 1-1 draw at Stoke.
Peter Crouch headed Stoke into the lead on nine minutes before Arsenal's newly-crowned Footballer of the Year Robin van Persie levelled on 15 minutes with his 35th goal of the season in all competitions.
Arsene Wenger's men will guarantee their entry to next season's Champions League if they win their remaining games against Norwich and West Bromwich Albion.
With leaders Manchester United facing Manchester City on Monday, and Chelsea and Tottenham in action against QPR and Blackburn respectively on Sunday, Saturday's other games focused on the battle for survival.
Bolton's hopes of moving out of the bottom three were dashed after they could only draw 2-2 at Sunderland.
Aston Villa remain in the relegation mire after scrapping to a 0-0 draw in a nervy midlands derby with West Brom.
Elsewhere, Liverpool recorded only their second win in seven games as Luis Suarez's first hat-trick for the club helped them to a 3-0 win over Norwich.
Australian Tim Cahill compounded a miserable day for long-time Socceroos teammate Mark Schwarzer by poking a low volley past him as Everton scored four goals for the second straight week to crush Fulham 4-0.
After coming on as a second-half substitute for Darron Gibson, Cahill latched onto a scooped pass from Steven Pienaar in the 60th minute to round out an impressive Saturday afternoon for the hosts that kept David Moyes' team in seventh place.
Cahill celebrated his third goal of a testing season in customary fashion, pummelling the corner flag.
A bizarre game at the Liberty Stadium, relegated Wolves fought back from 3-0 and 4-1 down to grab a 4-4 draw against Swansea.
-AAP