Yin holds a PhD in engineering from Tsinghua University and a master's degree in public administration from Harvard University.
He had previously worked for the State Administration of Foreign Exchange - the foreign exchange regulator, and an arm of the central bank, responsible for managing the country's foreign exchange reserves.
His predecessor, Guo, became vice central governor in February 2015, and had been responsible for anti-money laundering operations.
Though no reason was given for his departure, Guo turned 60 this year - the normal retirement age for officials of his rank.
Central bank chief Zhou Xiaochuan has been promoting a number of influential scholars to senior positions to beef up the central bank's management.
Yi Gang, a renowned economist who has a PhD from the University of Illinois, is a deputy central bank governor.
The cabinet said on Tuesday it had appointed Liu Guoqiang as an assistant governor at the central bank, replacing Yang Ziqiang.