The decision was made after a 3-0 defeat to Nam Định on Sunday, dropping Sài Gòn to 11th place in the V.League 1 table.
While Sài Gòn contended for the title last season and finished third, no less than 20 players left the club in the last off-season.
After being appointed to replace Vũ Tiến Thành to manage the club in late February, the 54-year-old three straight losses to HCM City FC, Becamex Bình Dương and Nam Định.
Shimoda was born in 1967 and speaks fluent English, Portuguese and Spanish. He was the technical director of the Kyoto Purple Sanga FC, then assistant technical director at FC Tokyo from 2001 to 2005.
From 2009 to 2016, he held many important positions at the Japan Football Association (JFA), including technical director for 2014-2016 as well as director of the U23, U19, U16 and the Japan national teams.
During his time, Japanese football achieved big success such as winning the 2011 Asian Cup, the Asian U23 Championship 2016, the Asian U19 Championship 2016 and reaching the Olympic semi-finals in 2012.
New coach Phương is expected to make his debut in the next match when Sài Gòn FC face defending champions Viettel at Hàng Đẫy stadium on April 3. VNS