A Qatari diplomat said on Wednesday that all Tunisian embassy staff left the country last Thursday.
Aljazeera, which has its headquarters in the Qatari capital, Doha, had aired two interviews with Moncef Marzouki, an opposition activist based in Paris who called for a "civil resistance" movement against the Tunisian government.
The Tunisian foreign ministry released a statement on Wednesday accusing Aljazeera of waging a "hostile campaign aimed at hurting Tunisia" and "turning its back on truth and objectivity every time it deals with news in Tunisia".
"By taking deliberately malicious positions vis-a-vis Tunisia, Aljazeera has broken all limits and transgressed the moral rules on which journalism is based," the statement said.
It said that the embassy closure was directed at Aljazeera and did not reflect on Tunisia's relations with Qatar, which it called a "brother nation".
In the past, Arab governments in Libya and Morocco have also briefly recalled their ambassadors from Qatar to protest against Aljazeera broadcasts.
Other Arab states such as Saudi Arabia and Bahrain have banned the station's correspondents.
In August 2004, the Iraqi government closed Aljazeera's Baghdad office. The office remains closed, but the station operates in the Kurdish-ruled area of the north.
Aljazeera, viewed by millions across the Arab world, is praised for being a rare independent voice among the Arab media, which are frequently government controlled.