The 30-year-old accountant from Wagga timed her sprint perfectly to take out the women's elite criterium on the Sturt St circuit in Ballarat.
Mackay only took up cycling seriously less than five years ago.
The only previous win in her career was the 2013 NSW road championship and she was surprised as anyone with Wednesday's win on day one of the nationals.
"Once I got on the podium, it was more disbelief," she said of her initial emotions.
"I'm probably going to have a bit of a name to live up to, so I'd best lift my game.
"It's is a huge step, hopefully, in the right direction as far as my cycling career goes."
Orica-AIS, the women's arm of Orica-GreenEDGE, had controlled the 33km race perfectly.
They had four riders out of the nine in the front group at the finish and planned to set up the final sprint for 2014 criterium champion Sarah Roy.
Crucially, their main rival and defending champion Kimberley Wells was also not in the break.
Mackay was last or second last among the leaders coming out of the last corner, but six months of sprint training then paid off.
"All I was thinking was just 'hunt them down, hunt them down, hunt them down'," Mackay said.
Mackay rang her mother before the victory ceremony and plans to celebrate her massive win.
"I don't think I will sleep very well at all - a lot of phone calls and hugs and hopefully a celebratory beer," she said.
"There were a few choice words that came out of her (mother's) mouth when I told her I won.
"She was fairly disappointed she wasn't here to see it.
"But she can watch the replays."
Second across the line was Orica-AIS rider Lizzie Williams, who was supposed to lead out Roy in the final sprint.
Lauren Kitchen finished third for the third year in a row.
Williams and Mackay were teammates two years ago at Specialized in the national road series.
"Sophie did a fantastic ride," Williams said.
"She's a quiet achiever - she's just a workhorse.
Williams also admitted to unease about the Orica-AIS post-race meeting.
"I'm a little bit scared to go back and face the coach," she said.