It was Byfield's - and Rotherham's - third goal of the season, as the Yorkshire outfit struggle in the lower reaches of Division One.
Gillingham could have led earlier when leading scorer Marlon King went close to an opener after 14 minutes as he hunted his fourth goal of the season.
A reckless high kick from Andy Monkhouse gave Gillingham a free kick in a dangerous area 25 yards out and King curled a low shot round the wall that needed a good save from Mike Pollitt, diving full stretch low to his left.
A minute later Andy Monkhouse had two quick opportunities. He should have scored but his first shot was blocked after Chris Sedgwick's cross from the right and his follow up attempt was deflected over.
The Gills suffered a blow when striker King limped off after pulling a hamstring.
But the visitors were untroubled by his departure and went ahead after 36 minutes through Danny Spiller.
Wayne Brown's long free kick in the area had Rotherham in trouble and as they failed to clear Spiller reacted first to pounce on the loose ball and hook it past Pollitt with an acrobatic overhead kick.
Byfield, scorer of Rotherham's only league goals of the season, had two chances early in the second half.
The Jamaican international twisted and turned but rifled his shot straight at the keeper and then, when Sedgwick broke on the right and crossed, Byfield scuffed his shot and Jason Brown had a comfortable save.
Substitute Paul Warne arrived after 69 minutes and almost had an immediate impact. His diving header seconds later was over the top and then a minute after that he stabbed a shot that went close.
Gills keeper Brown preserved his side's lead with a fine save, diving high to his left when Carl Robinson, on loan from Portsmouth, curled in a clever free kick.
But then 11 minutes from the end Scott Minto was brought down in the area by Nyron Nosworthy and Byfield grabbed the equaliser from the penalty spot.
Rotherham: Pollitt, Scott, Swailes, McIntosh, Minto, Sedgwick, Talbot, Robinson, Monkhouse, Byfield, Butler. Subs: Montgomery, Robins, Hurst, Warne, Richard Barker.
Gillingham: Jason Brown, Nosworthy, Cox, Hope, Wayne Brown, Spiller, Saunders, Smith, Perpetuini, King, Sidibe. Subs: Bossu, Hills, Ashby, Leon Johnson, Benjamin.
Referee: M Fletcher (Worcestershire)