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The Al Aqsa mosque represents Islam's third-holiest site.
"The president [Abbas] expressed his strong rejection and condemnation of the incident at the blessed Al Aqsa Mosque and his rejection of any act of violence from any side, especially in places of worship", WAFA said.
The site is administered by the Islamic Waqf organisation. Israel Police spokeswoman Luba Samri said guns were found in their possession.
Following the shooting, Israeli forces blockaded the mosque compound, not allowing worshippers into the area.
The incident occurred just before Friday prayers, usually attended by thousands of Muslims. They said they were still working to identify the attackers.
The attackers ranged in age from 19 to 29.
Friday noon prayers mark the highlight of the Muslim religious week.
Shortly after 7:00 AM, the terrorists went to the tribal gate and fired at the policemen who were at the time, and later the terrorists fled back to the Temple Mount area.
The Mount is the holiest site in Judaism.
Following the attack, Israeli police cleared the Al-Aqsa mosque and closed it for public.
With the shrine off limits, the faithful lined up near Damascus Gate and other entrances to the Old City.
Israeli police later ordered the closure of the compound, saying there would be no prayers at the site on Friday.
Police spokesman Mickey Rosenfeld confirmed to Newsweek that two officers died on Friday morning after suffering critical injuries in the attack.
Abbas made a rare phone call to Netanyahu, demanding he cancel the decision to close the Temple Mount to worshipers following a deadly terror attack on the site.
The video appears to show Israeli forces responding to the scene of the crime. The troops gave chase, engaged and shot the terrorists dead inside the complex.
The Temple Mount/Noble Sanctuary site is frequently a place of conflict and tension.
Private U.S. citizens should "take into consideration these restrictions and the additional guidance contained in the Department of State's travel warning for Israel, Jerusalem and the West Bank when making decisions regarding their travel in the Old City and in Jerusalem", the statement also read.