The 45-year-old former Latvia boss replaces Brian Tinnion, who quit after a humiliating 7-1 loss at Swansea City.
Assistant manager Keith Millen has been in temporary charge of the side following Tinnion's resignation.
Johnson was unveiled at a press conference on Friday afternoon, after agreeing terms on a compensation fee to be paid to Yeovil.
His first task will be to take charge of the side, currently second bottom of the table, as they travel to face fourth-placed Brentford on Saturday.