She said the driver, Brett McCullough, had lived just 15 minutes from the crash site at Carmont, near Stonehaven.
Ms Gilruth told MSPs: “He was only 45 and had moved from Kent to make his life in Aberdeenshire.
"He had been a train driver for six years and was very popular at the Aberdeen depot.”
The minster said one of the most most important findings of the final report by the UK Department for Transport’s Rail Accident Investigation Branch (RAIB) published today was “there was nothing in the way that Brett McCullough was driving the train which caused the accident – he was driving within the rules and instruction given to him”.
“Donald Dinnie [the conductor] was 58.
"His RMT [Rail, Maritime and Transport union] branch in Aberdeen paid tribute to him as someone who lit up the room with funny stories and wit.
"Christopher Stutchbury was 62. He came from Aberdeen and was an integral member of the Targe Towing Team, as well as a volunteer at a specialist palliative unit.
“All three were beloved family men who are sadly missed by their relatives, friends and colleagues.
She told MSPs: "On behalf of everyone in the Scottish Government and I am sure in this chamber, I want to share my profound condolences to these men’s families and friends for their loss.
“I have offered to meet with all of the families, at any time now or in the future, whilst appreciating that nothing I can say as minister can possibly erase their grief.
“The derailment that day also resulted in injuries, some of them serious, to six passengers and staff.
"I want to convey my sympathies to everyone affected and hurt.
"That includes the wider local community and the railway family.
“The shock of the impact of this accident was widely and keenly felt – and I know it continues to be so.”
Mr Dinnie’s family said: "We are very grateful for the way the RAIB has painstakingly handled this investigation and our thanks go to them for their diligence and consideration in reaching their conclusions.
"For us, whilst losing a loved one in these dreadful circumstances has been totally devastating, we also reflect that this accident happened at a time when the early stages of the pandemic saw fewer people travelling.”
Network Rail chief executive Andrew Haines said the report showed there were “fundamental” lessons to be learned, but “it should not have taken this tragic accident” to highlight them.
He said: “We must do better and we are utterly committed to that", and expressed “our deep sorrow and regret” at the three deaths.
Mr Haines said similar locations had been inspected and two independent taskforces were investigating extreme rainfall events and better drainage management.
ScotRail chief operating officer Ian McConnell said: “This report makes for very sober reading.
“ScotRail will play its part fully in ensuring safety lessons are learned.
“Our thoughts and prayers remain with the families, friends, and colleagues of Brett, Donald and Christopher.”