Cemil Cicek, the deputy prime minister, and Bekir Bozdag, a senior politician from the AKP delivered their arguments to judges in a closed session.
"From now on, it is up to the constitutional court," Cicek said as he left the court house.
He gave no details of the party's defense, but said he told the court that a quick decision would help the government to see its future.
On Tuesday, Abdurrahman Yalcinkaya, the chief prosecutor, had argued before the 11-judge tribunal that the AKP should be banned for threatening one of the basic tenets of the republic.
Hoda Abdel-Hamid, Al Jazeera's correspondent in Ankara, Turkey's capital, said: "The defence's positions is that... 90 per cent of the [chief prosecutor's] arguments are based on the statements made by members of the AK party either to the press or in speeches."
"The defence team argued that you really can't judge a party or people on intentions and it actually has to be [based on] some acts," she said.
"But they do acknowledge that the situation for them is very difficult."
Politically motivated
Yalcinkaya launched proceedings in March, accusing the AKP of gradually seeking to replace the secular system with Sharia [Islamic law].
He also asked the court to bar 71 AKP officials, including Recep Tayyip Erdogan, the Turkish prime minister, and Abdullah Gul, the president, from party politics for five years, in line with Turkish law.
The AKP, the offshoot of a now-banned Islamic movement, rejects the charges and says the case is politically motivated.
The popular party was re-elected to office last year with 47 percent of the vote.
After Thursday's hearing, a court-appointed rapporteur will prepare a non-binding report on what verdict the judges should give.
The court will then set a date to debate the case behind closed doors and reach a decision.