The central bank has faced pressure in the past from President Recep Tayyip Erdogan to lower interest rates to revive an economy which slipped into recession earlier this year.
In his first remarks, the new governor Uysal said he would continue to implement monetary policy independently and in line with his mandate and authority.
Cetinkaya had hiked the benchmark interest rate by a total of 750 basis points past year to support the ailing lira, pushing it to 24 percent by September where it has since been left unchanged.
Uysal's appointment also drew criticism from former central bank officials, who said laws that guarantee the regulator's independence also make it impossible for the executive branch to remove the governor unless he is involved in prohibited activities, such as holding shares in a commercial lender. He had described the interest rates as the "mother and father of all evil" and claimed that high interest rates cause inflation and that lowering them will improve growth.
Erdogan's ruling Justice and Development Party has built its success on Turkey's strong growth, with supporters boasting of progress in living standards during the Turkish leader's 16 years in office - first as prime minister and then president.
Governor Murat Cetinkaya, whose four-year term was due to run until 2020, will be replaced by his deputy Murat Uysal, a presidential decree published early on Saturday in the official gazette showed.
Erdogan, whose son-in-law is the finance and treasury minister, repeatedly criticized the central bank for keeping rates high.
Last month, Erdogan said the current rate was "unacceptable", promising to find a solution as soon as possible.
The decision came days after Turkey's inflation slowed to about 15 percent, allowing policy makers more room to start an easing cycle.
However, Cetinkaya's sacking comes just days before Turkey is expected to take delivery of Russian air defense systems, triggering likely US sanctions which could put the lira under renewed pressure.
"Those who removed the central bank governor overnight have lost the right to demand confidence in the country's economy".
Turkish inflation fell to 15.72 percent in June from 18.71 percent in May, official statistics showed on Wednesday, the lowest rate in almost a year.