The Scottish coach, 46, completes the move amid competition from other Premier League clubs and Saudi Pro League side Al Nassr, both of whom had shown interest before Chelsea moved.
MacPhee spent five seasons at Villa Park, joining in August 2021, and has also been working with the Portugal national team for the past five years under Roberto Martinez, who resigned after this summer's World Cup, in which Portugal lost to eventual champions Spain in the last 16.
Before Aston Villa, MacPhee built his reputation working as a set-piece specialist with Northern Ireland, Scotland and Hearts, as well as a spell with Danish side Midtjylland, having started his coaching career as an assistant at Cowdenbeath and St Mirren.
MacPhee helped Villa score more goals from set-pieces than any other team in Europe's top five leagues during the 2023-24 season, with the club scoring 74 set-piece goals across his time there.
They followed that by ranking among the top five a season later and finished joint-top with Arsenal in the Premier League last season, with 29 set-piece goals, despite Villa finishing fourth in the table to Chelsea's tenth. Villa made attempts to keep MacPhee at the club but were unable to persuade him to turn down the move.
New Chelsea manager Xabi Alonso has space in his current backroom staff as previous set-piece coach Bernardo Cueva, who joined from Brentford for £750,000 in 2024, is moving away from a touchline role into a more behind-the-scenes position.
MacPhee's arrival adds Premier League experience to a coaching group Alonso has otherwise stocked with former Spanish colleagues, including Alberto Encinas, Beñat Labaien, Luis Llopis and Miguel Muñoz. Chelsea signed Morgan Rogers from Aston Villa for £117m this week, with Alejandro Garnacho moving in the other direction on an initial loan that will likely become permanent through an option to buy.