Millwall's hopes of recording a first Championship win in six games were shattered at a rain-soaked Reebok Stadium.
The Lions went into action on the back of three draws and in confident form against a Trotters side yet to record a victory on home turf this season.
Boss Steve Lomas made four changes to the side that started against Burnley last weekend with Justin Hoyte handed his debut in a defence that also saw Shane Lowry come in for the injured Scott Malone at left-back.
Jimmy Abdou slotted into midfield following his one-match ban with Jermaine Easter completing the quartert of changes, starting up front instead of Scott McDonald who failed a late fitness test after picking up an injury in training on Friday.
The Lions found themselves behind in controversial circumstances with barely five minutes on the clock. For the second time in as many games, Nicky Bailey was lying on the ground with a head injury while play continued around him. Bolton took full advantage of the extra man in the middle and Lee's ball from the left picked out Rob Hall who beat David Forde with a low angled drive while Bailey was still down.
Spurred on by a real sense of injustice The Lions fought their way back on to level terms just before the half-hour mark when a fine ball from Lowry picked out Easter in a central position. The Welsh international striker took one touch to control, spun and despatched a crisp, rising shot that gave Andrew Lonergan no chance in the Bolton goal.
The Lions enjoyed plenty of possession and Martyn Waghorn twice went close to putting the visitors ahead with a long-range shot that flew wide and then a second effort blocked by Tim Ream.
Although it was Millwall who looked the more likely of the two teams to score, it was in fact Bolton who edged ahead moments before half-time when Beckford, looking marginally offside from Ream's pass, kept his cool to loft the ball over Forde and into the back of the net.
After the restart the game shaped up in a similar fashion to the first with Millwall asking plenty of questions of a Bolton defence that seemed content to sit back, soak up the pressure and try to hit their opponents on the counter-attack.
Waghorn was close to grabbing a leveller on 54 minutes with a firm header from Lowry's deep cross that was pushed behind at full stretch by Lonergan.
Another inviting delivery from the left by Lowry was gathered at the second attempt by the keeper as The Lions continued to push on.
Bailey fired narrowly over after Waghorn's corner had been headed into his path by Danny Shittu as Millwall pressed in search of that elusive second goal.
But it was Bolton who put the game beyond reach in the last minute of normal time courtesy of sub Andre Moritz, who powered through the visiting defence and drove home a third, killer goal.
Lonergan, Baptiste, McNaughton, Ream, Mills, Danns, Spearing, Medo, Lee (Knight, 78mins) , Beckford (Davies, 83mins), Hall (Moritz, 60mins). Subs not used: Lee-Barrett, Eagles, Ngog, Threlkeld.Bolton Wanderers:
Hall (5mins), Beckford (43mins), Moritz (90mins)Scorers:
Forde; Hoyte, Robinson, Shittu, Lowry; Abdou (Morison, 75mins), Bailey; Waghorn, Trotter, Woolford Martin, 79mins); Easter (Feeney, 59mins). Subs not used: Bywater, J.Smith, Chaplow, Beevers.Millwall: