Mr Mugabe had been under house arrest for days. The army made its move after a power struggle over his successor.
The military said on Friday it was "engaging" with Mr Mugabe and would advise the public on the outcome of talks "as soon as possible".
Mr Mugabe's attendance at the graduation is an annual tradition but few expected to see him there, the BBC's Andrew Harding reports from Zimbabwe.
Mr Mugabe walked slowly up a red carpet and joined the crowd in singing the national anthem, then opened the graduation ceremony at Zimbabwe's Open University, where he is chancellor.
One of the people he conferred a degree upon was Marry Chiwenga, the wife of the general who detained him on Wednesday, the state broadcaster reports.
Neither the 93-year-old president's wife, Grace Mugabe, nor Education Minister Jonathan Moyo - an ally of hers whose house was reportedly raided by the military - were present.
The army acted after Mr Mugabe sacked Vice-President Emmerson Mnangagwa last week.
Mr Mnangagwa was seen as a potential successor and his sacking paved the way for Grace Mugabe - who is four decades younger than him - to take over the presidency instead.
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