The remains of Jim and Ann McQuire, from Cumbernauld, North Lanarkshire, and Billy and Lisa Graham, from Bankfoot, near Perth, arrived back in the UK yesterday.
They were among 38 people killed by gunman Seifeddine Rezgui when he opened fire on holidaymakers on a beach in the resort of Sousse last Friday.
Today, the Queen and the Duke of Edinburgh observed the silence while on a visit to Strathclyde University.
At midday, they paused along with students and university principal Professor Sir Jim McDonald.
A church service was held in Cumbernauld in memory of the McQuires while a candlelit vigil is planned later in Perthshire for the Grahams.
Both North Lanarkshire Council and Perth and Kinross Council are flying flags at half-mast and books of condolence have been opened.
Passengers at the normally bustling check-in area of Glasgow Airport fell silent, most standing with heads bowed, to observe the minute’s silence.
Flags are also being flown at half-mast at the Scottish Parliament in Edinburgh.
The silence was also observed at the Appeal Court in Edinburgh where a hearing was taking place to decide whether relatives of Lockerbie bombing victims could pursue a posthumous appeal on behalf of Abdelbaset al-Megrahi, the only man convicted of the atrocity.
add to Tunisia silence
First Minister Nicola Sturgeon also paid her respects when she signed a book of condolence.
Ms Sturgeon joined local representatives at the headquarters of North Lanarkshire Council in Motherwell to observe the silence and pay her own tribute to both the Scottish families as well as the other victims.
At the same time, Deputy First Minister John Swinney travelled to Perth and Kinross to pay his respects by signing the book of condolence in the local authority offices in Perth.
The First Minister said: “Today is a day to remember all of the victims of this senseless and cowardly terrorist attack and my thoughts, prayers and heartfelt condolences are with their families and friends at this incredibly difficult time.
“I hope that the families of James and Ann McQuire, from Cumbernauld, and Billy and Lisa Graham, from Bankfoot, can take some comfort from the fact that right across Scotland people have come together to condemn these mindless acts and pay respects to their loved ones during today’s minute’s silence - just as I hope all the bereaved families will take comfort from the expression of solidarity right across the UK.
“We will continue to offer all the support we possibly can to those affected and I hope now that the privacy of the families will be respected in order that they can mourn their loss in peace.”