In 2013, Hore had made an agreement with then Acting Commissioner Ivan Pillay to stay on as COO until a new permanent Commissioner was appointed.
Hore joined SARS in 2006.
SARS Commissioner Tom Moyane thanked Hore for his commitment and diligence at SARS.
"He has played an instrumental leadership role in implementing a comprehensive modernisation programme that has transformed SARS operations from a largely paper-based operating system to an almost completely automated environment with significant benefits to both taxpayers and the institution," said Moyane.
SARS said it will endeavour to find a suitable replacement for the vacancy.
"I am extremely proud of what we as an institution have accomplished. The SARS modernisation journey towards a mostly digital operating environment has positioned it as a global leader in the use of technology.
"The ability to build a team that has operated at the highest levels of proficiency in this complex environment is, for me, one of the greatest achievements," said Hore.
Moyane has appointed Jonas Makwakwa, the Group Executive for Audit, as acting chief operations officer.
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