Lee's magnificent solo effort in the 33rd minute put Bolton 2-1 ahead after Marco Alonso had cancelled out an early header from Nikola Zigic, who was later sent off.
A late penalty from Keith Andrews wrapped up a vital three points for Wanderers following two successive defeats.
Freedman said: "It was a wonderful goal from a wonderful player and he deserves all the credit he gets because he had a horrible injury and he's worked so hard to get back from it.
"Today we put everything together and to do it in front of the home fans is all the more pleasing.
"We targeted the midfield as an area where we could dominate the game today and we certainly did that throughout.
"We moved the ball around well and to get the win was great for everyone."