The Macron Stadium outfit have experience an upturn in form since Neil Lennon took the reins in October, and maintained that upward curve with a narrow victory at The Den on Friday.
Former Swansea City man Pratley got the first sight of goal - firing just wide of the target after eight minutes.
The 29-year-old tested goalkeeper David Forde with low strike shortly after the half-hour mark, but Pratley had to wait until after the interval to get his name on the scoresheet.
The midfielder showed great patience and poise as he took the ball around defender Danny Shittu, before rifling in off the underside of the crossbar.
Victory sees Bolton climb to 14th ahead of the weekend fixtures, while Millwall are now in danger of slipping below Rotherham United into 21st.
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