Andre Moritz added a third goal in the last minute of normal time to secure the victory for Dougie Freedman's men and extend their unbeaten run to five games.
Former West Ham winger Hall opened the scoring for Wanderers early on before Jermaine Easter levelled for the Lions.
But Beckford put the Trotters back in front before half-time and Moritz got his first goal for the club to confirm the victory which sees them leapfrog their opponents in the table.
Despite scoring in last week's win at Bournemouth, Freedman opted to start Hall in place of David Ngog in the only change to his starting line-up.
Liam Feeney, who recently returned to Millwall after a loan spell at Bolton, featured on Steve Lomas's bench, with Justin Hoyte making his debut after signing on loan from Middlesbrough.
Hall looked dangerous from the off and forced a smart save from David Forde after a dazzling run into the box in the fourth minute. Just a minute later, the Wanderers winger then broke the deadlock.
Neil Danns played the ball into Beckford, who produced a delightful flick to Chung-Yong Lee.
The South Korean international then found Hall, who stroked the ball past Forde into the bottom right corner to complete a well worked team goal.
Hall then taunted the travelling Lions fans and that was not the only thing that the visitors were aggrieved about.
At the time of the goal, Nicky Bailey was taken off the pitch after a head injury and was not allowed back on until after the ball was in the back of the net.
Millwall then hit back in the 28th minute, as Shane Lowry slid a ball into Easter's feet in the penalty area. Easter then calmly controlled the ball and slotted in past Andy Lonergan for the equaliser.
The Bolton fans in the Reebok thought that their team had regained the lead moments later. Beckford hit a ball on the bounce which looked to have gone in but just hit the side netting.
But the Jamaican international was consistently given the space to run in behind by the Millwall defenders. Two minutes before half-time, he punished them.
Tim Ream produced a sublime defence-splitting pass to Beckford, who stylishly chipped over Forde to put them back in front two minutes before the break.
Beckford and Hall both came off as Wanderers tried to see out the match for the win.
But they still proved to be a threat on the counter in the second half.
Moritz's goal epitomised that as the Brazilian attacking midfielder stepped over past the backtracking Lions defenders and rocketed the ball past Forde to put the icing on the Trotters cake.