Flags on Edinburgh Castle were also flown at half mast to honour the duke, who passed away aged 99 last week.
Leading the minute’s silence, Frank Ross Lord Lieutenant – the Queen's representative in Edinburgh – stood outside City Chambers at 3pm as the duke’s funeral began.
On Friday, the Lord Provost led a special motion in honour of Prince Philip, paying tribute to his life and the “immense contribution” he made to the civic life and international reputation of Edinburgh.
In his motion, councillor Ross said: "He demonstrated great appreciation of and support for Scotland’s Capital City and its citizens. Quite simply, he took the name of our Capital across the world and put Edinburgh on the map in so many ways.”