The 27-year-old will join Ian Holloway's men on a two-year deal.
He becomes the third new arrival at The Den this summer following the acquisitions of Carlos Edwards and Lee Gregory.
"I can't wait to get started," Byron told the Millwall website. "And to start the season with a game against Leeds, my home-town club, is going to be great."
He will come across at least one familiar face in south London in the shape of former Yeovil team-mate Ed Upson, who made the move from Huish Park in January.
"I spoke to Ed and he's being giving me a heads up and speaks very highly about the club. I'm just really looking forward to starting on Thursday."
Webster began his career at York in 2004 and after three years he joined Czech side FK Banik Most, where he played for two seasons.
The towering centre-back joined Doncaster in 2009 but after loan spells at Hereford and Northampton he agreed a permanent switch to the Cobblers in 2011.
It was at Sixfields that Webster first played under Gary Johnson, who brought him to Yeovil a year later. He was a mainstay of the Glovers defence which helped secure promotion to the Championship during the 2012/13 campaign.
The 6'5" defender made 45 appearances for Yeovil in their first-ever season in the second tier of English football, scoring four goals.