The previous two nominees of Prime Minister Yasuo Fukuda's government for the top post at the Bank of Japan were rejected by the upper house, which is controlled by opposition parties. Fukuda's coalition government enjoys a big majority in the lower house.
In the absence of a governor the past three weeks, Shirakawa had been acting in that position, Kyodo news service reported.
While Shirakawa's nomination was cleared, the upper house voted down Hiroshi Watanabe, former vice finance minister for international affairs, for one of the two central bank deputy chief posts, Kyodo said.
The appointments of governor and deputies require the approval of both houses of Parliament.
Shirakawa's approval also comes just in time before the Friday meeting of the financial heads of the Group of Seven countries in Washington, D.C.