A calmly taken penalty gave Byfield his 12th goal of the season and rounded off a stirring comeback after Oldham took the lead on 55 minutes.
John Sheridan's Latics were badly hit by injury and suspension with centre-back Sean Gregan, left-back Simon Charlton and midfielder Richie Wellens all missing from their regular first choice team.
And Millwall cashed in to continue their rise up the table. The Lions have won seven of their last nine games and are not yet giving up hope of a play-off place.
Oldham paid for missed chances with the most glaring coming from the usually reliable Chris Porter who has scored 20 times this season.
Millwall did not create many openings themselves but they were clinical with those which came along.
The visitors threatened early on when winger Tom Brighton dashed into space at the near post and sent his header just a foot wide of the target.
But Oldham were on top during the first half as Paul Warne headed at keeper Lenny Pidgeley and Andy Liddell sent a long-range free-kick narrowly wide.
Porter's miss came on 24 minutes as he ran through after a pass from Craig Rocastle but could only shoot straight at Pidgeley from near the penalty spot.
Warne blasted over before the home team grabbed their lead from a neat passage of play.
The final ball was sent over by Neal Eardley and Warne sent his ten-yard header into the bottom corner to give the keeper no chance.
Oldham, however, were pegged back within seconds of Millwall manager Willie Donachie introducing Marvin Williams into the action.
Williams made it 1-1 with a close-range finish after being released by the dangerous Byfield.
Byfield himself headed over but he snatched the crucial goal after Poul Hubertz saw his shot from the edge of the box handled by Stefan Stam.
Byfield slotted his penalty low down the middle of the goal as Oldham keeper Les Pogliacomi dived away to his right.