"We will continue on our path, with a new enthusiasm, with the new blood that we have brought in"
Tayyip Erdogan, prime minister
Gul's original candidacy in April had also sparked months of political turmoil in Turkey after secularists opposed the move.
The AKP, whose roots lie in political Islam, describes itself as a conservative, pro-Western party.
However, secularist Turks say that the party's leadership is committed to an Islamist agenda.
The line-up continues the direction set by his ally Recep Tayyip Erdogan, the prime minister, who had proposed the team.
Erdogan said he prepared the new line-up with "the skills to realise our goals in the coming period".
"We will continue on our path, with a new enthusiasm, with the new blood that we have brought in. We have formed a strong team," he said after the list was approved.
As foreign minister in 2005, Gul helped Turkey get into EU accession talks, and has declared his intention to continue actively in foreign affairs.
Ali Babacan, his US-educated successor, will keep his role as chief negotiator in the membership talks, which were partially frozen last year.
Gul, 56, is the first politician with a background in political Islam to become president in a mainly Muslim but constitutionally secular country.
|A series of reports on Turkey's political landscape|
His appointment irritated the powerful military which has vowed to safeguard Turkey's secularism.
The military has ousted four governments in the past 60 years.
Senior generals snubbed Gul's swearing-in ceremony in parliament on Tuesday, widely-seen as a sign of protest against their new commander-in-chief.
On Monday the military's top brass hinted that it would not stand on the sidelines if the separation of religion and state was threatened.
Gul has denied any intention to subvert the secular order, pledging in an inaugural speech to uphold the system and the principles of Mustafa Kemal Ataturk, founder of modern Turkey.
Meanwhile, in central Ankara, trade unions continued protests on Wednesday demanding better pay, jobs for millions of poor and a solution for the country's water shortages.