The midfielder outshone returning Wanderers hero Eidur Gudjohnsen as the visitors collected only their second victory on the road this season – making it seven matches unbeaten overall – and climbed to 14th in the table.
Gudjohnsen was handed his first start since rejoining the club he left 14 years ago for Chelsea, but the 36-year-old striker had departed the field by the time Pratley crashed in a fine second-half winner.
Gudjohnsen did have half a chance in the opening five minutes, when Lee Chung-Yong’s cutback reached him on the edge of the area, but the Icelander could not get his shot away in time.
Instead Lee was Bolton’s main attacking threat and he got behind the Lions defence again moments later, only for Pratley to head his cross straight at Millwall goalkeeper David Forde.
Forde also kept out Tim Ream’s header from the resulting corner, and denied Rob Hall and then Pratley following another mazy run from Lee.
Yet despite Bolton dominating possession, the best two chances of the first half fell to Millwall. First, winger Magaye Gueye’s fine ball sent Lee Gregory between the Bolton centre-halves, but the striker, who hit the Lions’ winner at Brighton last week from a similar range, this time dragged his angled shot wide.
As half-time approached Andy Wilkinson’s cross from the right found Angel Martinez, but the Spaniard’s volley flew inches past Andy Lonergan’s left-hand post.
There was controversy just after the interval, when Forde’s long clearance sent Gregory racing through again. Gregory got to the ball before Lonergan and touched it towards goal before tumbling over the onrushing keeper’s challenge, but referee Stuart Attwell ignored Millwall’s claims for a penalty.
There were more penalty appeals moments later, when Scott Malone hit the deck in the area, but Attwell waved play on again.
Bolton winger Hall was somehow denied a goal on the hour mark, when his shot cannoned off the inside of the post, flew along the line and off Forde’s leg before rolling to safety.
But Pratley struck in the 68th minute, when he collected Lee’s fine pass, beat Danny Shittu on the edge of the area and arrowed his shot past Forde and into the net.
Martyn Woolford could have equalised with five minutes remaining, but Lonergan was out quickly to block his shot as Bolton held on for the three points.