Lee struck after 108 minutes of the AFC Asian Cup Qatar 2011™ final when he volleyed home Yuto Nagatomo's left-wing cross.
Australia, though, had their chances to claim a maiden continental triumph and will reflect on Harry Kewell's second-half miss when one-on-one with Japan keeper Eiji Kawashima as particularly crucial.
The Socceroos had the game's first opportunity when following a slick move, Carl Valeri fed Matt McKay but he sliced wide of the far post.
Mark Schwarzer then almost presented Japan with the opener when he tried to prevent the ball going behind for a corner but only succeeded in kicking it straight to Nagatomo but the defender's long-range effort sailed over the bar with David Carney scrambling back to cover.
McKay's neat backheel released Brett Holman down the right but nobody could get on the end of the winger's fizzing low cross before Japan keeper Eiji Kawashima did well to push Kewell's close-range header away in the 18th minute after Tim Cahill had met Carney's corner on the far side of the box.
Kewell then guided Luke Wilkshire's cross from the right over the bar before the striker was off target from a narrow angle when he latched on to Cahill's knockdown from Neill's diagonal ball just after the half-hour mark.
Ryoichi Maeda was presented with a sight of goal nine minutes before the interval after Yasuhito Endo had laid-off Keisuke Honda's incisive pass into the forward's path but he fired over from just outside the box as the first-half ended goalless.
Australia came agonisingly close to taking the lead two minutes after the break when, after Kawashima misjudged Wilkshire's cross, the ball hit the bar and then Cahill but bounced up into Maya Yoshida's chest on the line as Japan cleared.
Kewell lashed over from inside the six-yard box before Japan almost broke the deadlock in the 65th minute when Nagatomo created a yard of space before delivering a beautiful left-foot cross that Shinji Okazaki glanced just the wrong side of the post with Schwarzer rooted to the spot.
Kewell then spurned the best chance of the game six minutes later when he latched onto a long ball and raced clear on goal but Kawashima denied him with an outstretched right leg.
The Japan keeper was alert to save at Kewell's feet after Yasuyuki Konno under-hit a backpass and Carney saw a shot inside the box deflected over the bar late on as normal time ended goalless.
Australia had two opportunities in quick succession in the first period of extra time. First, McKay played in Kewell but the ball broke to Brett Emerton, who curled a left-foot shot just wide.
Substitute Robbie Kruse then almost made an immediate impact but his header from Emerton's cross was clawed away by a desperate Kawashima from under the bar.
The winning goal finally came after 108 minutes when Nagatomo surged down the left and his cross picked out Lee unmarked eight yards from goal. The substitute waited for the ball to drop before executing a left-foot volley that gave Schwarzer no chance as it found the back of the net
The Australian keeper then held Endo's free-kick before Carney struck a set-piece into the wall from just outside the area as Japan clung on for a famous victory.