The 54-year-old was Southgate's right-hand man during his eight years in charge of England, a period which saw them reach two European Championship finals and one World Cup semi-final.
He has been out of work since stepping down along with Southgate following England's defeat to Spain in the Euro final in Germany in July.
Reports in Japanese media said Holland would take charge of Yokohama ahead of the new J. League season, which starts in February.
He watched from the stands as Yokohama lost 2-0 at home to Nagoya Grampus on Sunday in their final game of the 2024 campaign.
Yokohama finished ninth in the 20-team first division table.
Holland worked under several managers during eight years as a coach at Chelsea but his only previous experience in charge of a team was at Crewe Alexandra between 2007 and 2008.
Yokohama are part of City Football Group and were coached by Tottenham's Ange Postecoglou from 2018 to 2021.
They started the season with former Liverpool and Leeds forward Harry Kewell in the dugout but fired him midway through the campaign and put his assistant John Hutchinson in interim charge.
They reached the Asian Champions League final in May under Kewell but lost to Al Ain of the United Arab Emirates.
