The bill now returns to Sezer for signing.
He cannot veto the amendments a second time but can put them to a referendum.
Sezer said last week that the haste with which the reforms were introduced would lead to "a deviation from the parliamentary system" and "create far-reaching, irreparable problems".
Confident of win
Erdogan says he is confident of winning any referendum on the reforms, which also cut the term of the president's mandate to five years from seven and allow him to seek a second term.
They also reduce parliament's term to four years from five.
The main opposition party, the staunchly secular Republican People's Party (CHP), says it may challenge the amendments in the constitutional court beacuse of alleged balloting violations.
"Whatever system the Turkish majority want should be done through elections"
Baz, Vancouver, Canada
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The CHP argued that all seven provisions and the entire package had to get at least 367 votes, or a two-thirds majority, to be adopted.
The first article only got 366 votes, but the speaker rejected CHP's protests and went ahead with the balloting.
The government has argued that the reforms were necessary due to deadlock over the appointment of a new president.
Strong secularist opposition to the sole candidate, Abdullah Gul, the foreign minister from the ruling party, forced him to withdraw.
The AKP-majority parliament was virtually certain to elect Gul in later stages of the election, but the opposition boycotted two rounds of presidential balloting on April 27 and May 6, denying the house the numbers required for a valid vote.
The crisis was exacerbated by a warning from the military that it was ready to act to defend the secular system, and by demonstrations against the government.
Recent public opinion surveys have shown that, despite the protests, Erdogan's party is still the most popular in Turkey, leading its rivals in the opposition by a wide margin.