Da Cruz was only unveiled by Amakhosi last week as replacement for co-coaches Cedric Kaze and Khalil Ben Youssef.
Mahmoud Abbas joined the Betway Premiership side after spells in Saudi Arabia with Al-Wehda, Al-Hazem and Al-Qadsiah.
Sheppard has worked at Amakhosi as assistants to Gavin Hunt, Arthur Zwane and Cavin Johnson, alongside his role in the club’s youth academy as reserve side.
Julien Le Heran has, meanwhile, also been confirmed as Chiefs’ new head of sport science.
Part of a club statement read: “Coach Sheppard will officially take on the role of second assistant coach, working alongside Coach Fernando da Cruz and Assistant Coach Mahmoud Abbas.
“He will [also] continue to serve as the vital link between the reserve side, where he collaborates with Coach Vela Khumalo, and the senior team.
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“Sheppard did similar work with the previous technical team, helping Amakhosi to finish third in the Betway Premiership last season.”
Sheppard holds a UEFA A License, but more recently completed his CAF A coaching course.
“We fully support the education and development of our coaches,” Sporting Director Kaizer Motaung Jr added.
“Having Coach Sheppy qualified to work at the highest level in Africa with his CAF A Licence, as well as in Europe with his UEFA A Licence, means our players – both in the Kaizer Chiefs Youth Development Academy and the senior team – will benefit greatly. We are proud and happy for him.”
A delighted Sheppard said on Soccer Laduma: “I’m proud to have achieved this. The journey started some time ago and came with challenges along the way, but I’m glad I’ve reached the goal.
“I’m grateful to the club for standing by me throughout the process, and I’ll work hard to share the knowledge I have acquired with our players and other coaches within the club.”