On Friday, a court ruled that Zaman, previously linked to an opponent of President Recep Tayyip Erdogan, should now be run by administrators.
Its last edition under old ownership on Saturday said Turkey's press had seen one of its "darkest days".
Meanwhile, a newspaper set up by former Zaman staff was launched on Sunday.
Police raided Zaman's Istanbul offices late on Friday hours after a court ruling placed it under state control, but managers were still able to get Saturday's edition to print.
No reason was given by the court for the decision.
Turkish Prime Minister Ahmet Davutoglu said the takeover was "legal, not political".
"It is out of the question for either me or any of my colleagues to interfere in this process," he said in a television interview.
Water cannon and tear gas were used against some 500 Zaman supporters gathered in front of its headquarters on Saturday.
Zaman journalists who arrived to work on Saturday said their access to internal servers had been denied. Its editor-in-chief Abdulhamit Bilici and a leading columnist were also fired