Brady not surprisingly missed his fourth straight preseason game with an injury to his right foot. The NFL MVP insisted earlier this week that he would be ready for the Patriots' season opener against the Kansas City Chiefs a week from Sunday.
Manning's absence was a surprise.
Coach Tom Coughlin had said the Super Bowl MVP would be out there for 10 plays in his final warmup for the NFL opener on Sept. 4 against the Washington Redskins at Giants Stadium.
However, the coach changed his mind before the game and sat Manning.
The decision came less than a week after the Giants lost two-time Pro Bowl defensive end Osi Umenyiora for the season to a knee injury against the Jets.
Manning out-dueled a harried Brady in the Giants' 17-14 win in the Super Bowl.
Manning completed 19-of-34 for 255 yards and two touchdowns, including a game-winning 13-yard touchdown pass to Plaxico Burress with 35 seconds to play.
Brady, who had guided the Patriots to a perfect season until the title game, was 29-of-48 for 266 yards with five sacks. His 6-yard touchdown pass to Randy Moss with less than three minutes to play appeared to have capped New England's perfect season, but Manning and the Giants rallied to spoil it.
Burress returned to practice this week after missing all of training camp with an injury to his right ankle.
Renaldo Wynn replaced Tuck at left end.