Andrei Kozlov, 41, who was in charge of supervising the central bank, was attacked by gunmen with automatic weapons as he arrived for an amateur football match at a sports stadium in the Russian capital on Wednesday evening.
Inna Sigeyeva, a deputy chief doctor at Moscow's Hospital No 33 said: "Andrei Kozlov died early this morning [Thursday]."
Kozlov had undergone emergency surgery overnight for serious gunshot wounds to his chest and head.
Sources close to police investigations said the attack on the banker, who had led an aggressive drive to shut down banks accused of money laundering and other crimes, bore the hallmarks of a contract killing.
Witnesses said the gunmen fired at least four times, also killing Kozlov's driver Alexander Semyonov
Yuri Syomin, Moscow's chief prosecutor, said: "We are looking at all possible versions, including [Kozlov's] professional activities, mistaken identity, and his personal relations."
Under Kozlov's supervision, the central bank cancelled the licences of a large number of banks that were suspected of involvement in money laundering.
At a banking forum last week in the southern city of Sochi he called for tougher penalties against bankers found guilty of such crimes.
Kozlov became the bank's first deputy chairman in 1997, then left two years later for a stint in the private sector.
He was reappointed to the job in April 2002.