But Vietnam fought back in the second half with sharp counter attacks while Japanese substitutes squandered scoring opportunities.
The Blue Samurai took off four Europe-based stars for players keen to prove themselves ahead of Tuesdays's home FIFA World Cup qualifier against Tajikistan.
The move almost backfired two minutes into the second half, after Vietnam midfielder Nguyen Trong Hoang stole the ball and rushed towards goal only to have his shot blocked by goalkeeper Shusaku Nishikawa.
The Vietnamese looked increasingly threatening, moving the ball quickly, while star striker Le Cong Vinh had a close-range header saved by the impressive Nishikawa.
After the game, Japan coach Alberto Zaccheroni said: "We wanted to test players whom we have not been able to use. We saw poor continuity."
Voicing his frustration, Lee admitted the performance was poor ahead of a crucial week for the Blue Samurai. "It was good that we won. But we need to improve our game," he said.