Lee's late strike keeps Valencia's European hopes alive
Lee, 19, clinched his side's first victory since Albert Celades was sacked earlier this month and sent his outfit up to eighth, just behind Real Sociedad in the spot for the qualifying rounds for next season's continental competition.
Uruguay's Maxi Gomez opened the scoring on the half-hour mark, finishing tidily at the back post from a low Kevin Gameiro cross.
Victor Garcia, making his maiden first-team appearance of the season having spent the campaign with the reserves, equalised for Valladolid just after the break.
Midfielder Garcia half-volleyed home a deflected shot after 100 seconds of the second half.
Lee claimed his second goal of the campaign with less than two minutes of normal time remaining.
His whipped shot from outside the box beat Antonito to end up in the bottom corner.
Later, third-placed Atletico Madrid visit Celta Vigo as they chase a place in next season's Champions League.