Japan recovered from Michael Owen's early goal to hold England 1-1.
Sven-Goran Eriksson fielded his first-choice line-up, including Frank Lampard, and England were given a stern test in a warm-up for Euro 2004.
Owen put England in front after 21 minutes when Seigo Narazaki fumbled Steven Gerrard's shot.
But Japan created chances and deservedly equalised seven minutes after half-time when Shinji Ono crowned a fine move with a crisp finish.
England ended with a couple of injury worries, David Beckham receiving treatment for an ankle injury and John Terry going off near the end with a hamstring problem.
Eriksson, as he hinted, played the team that is likely to start Euro 2004 against France, with Lampard getting the nod ahead of Nicky Butt.
And England almost got the perfect start after four minutes, when Japan goalkeeper Seigo Narazaki was fortunate to block Terry's header.
England's passing was impressive and they took a deserved lead after 21 minutes.
Gerrard's surging run from midfield ended with a shot that was only fumbled by Narazaki, which allowed the lurking Owen a simple tap in.
21 mins: Michael Owen puts England ahead
52 mins: Shinji Ono equalises for Japan
It sparked Japan into action, and David James was forced into saves from Keiji Tamada and Shumsuke Nakamura as they tried their luck from long range.
And Tsuneyasu Miyamoto should have levelled five minutes before the interval when he was allowed a free header from a corner but was wastefully off target.
Japan were unfortunate not to be awarded a penalty on the stroke of half-time when Paul Scholes hauled down Alex, but Roberto Rosetti waved away their appeals.
But there was no escape for England after 52 minutes when a slick Japanese passing move ended with Alex providing the perfect delivery for Ono to score through James' legs.
England responded when Wayne Rooney's pass released Owen, but he was denied by Narazaki's legs.
Eriksson made a triple substitution with 15 minutes left, sending on Emile Heskey, Darius Vassell and Kieron Dyer for Owen, Rooney and Scholes.
But it was Japan who continued to hold the upper hand, with James saving well from Alex's wicked drive.
England: James, Gary Neville (Phil Neville 85),
Terry (King 88), Campbell, Ashley Cole, Scholes (Dyer 77),
Beckham (Joe Cole 81), Gerrard (Hargreaves 82),
Lampard (Butt 82), Owen (Vassell 77), Rooney (Heskey 77).
Subs not used: Bridge, Robinson, Carragher, Walker, Defoe.
Japan: Narazaki, Nakazawa, Miyamoto, Tsuboi, Santos, Ono,
Inamoto (Fukunishi 90), Kaji, Nakamura, Tamada (Suzuki 60),
Kubo (Yanagisawa 60). Subs not used: Doi, Kawaguchi, Miura, Tanaka, Chano, Fujita,
Ogasawara, Endo, Motoyama.
Referee: Roberto Rosetti (Italy).