Otley rider Armitstead followed up her silver medal in the time trial event earlier last week by beating Wiggle Honda pair Laura Trott and Dani King by 63 seconds.
The 2011 champion, who has now finished in the top two for five years running, made her move in the penultimate of eight laps before streaking clear in the final round.
Amy Roberts of Wiggle Honda had pulled away in order to break up the group after a slow start but Armitstead was ultimately too strong.
The 24-year-old Boels Dolman rider said: “It’s really special. It was one of my main goals of the season.
“I’ve had an up and down season so far so I needed a bit of a confidence boost and hopefully having the jersey on my back will help.”
The circuit, which will be used for next year’s Commonwealth Games, started and finished in Glasgow Green and took the cyclists through the heart of Glasgow city centre and to the west end past Glasgow University.
Armitstead added: “With two laps to go I stuck one in just over the university climb. It was the longest and steepest. I managed to drop everybody but Laura was just close enough.
“I kind of did 80 per cent on that climb and unfortunately I dropped my team-mates so I was alone with two Wiggles.
“It was strange tactics from them in the final, they just rode it out. That was perfect for me. I gave it 100 per cent on the same climb and managed to get the gap.
“I’ve got a lot of experience on the road now and it’s their first real season on the road so I felt confident.”
Trott was delighted with her silver medal after beating team-mate King in a sprint finish and admitted Armitstead was the “stronger and better rider on the day”.
King added: “I am really happy. A couple of days ago I didn’t feel great after the time trial so if someone said to me you were going to get third today, I would have been over the moon.
“We worked well together, did everything we could and Lizzie was the better rider today. She won a silver in the Olympic games in the road race so I don’t think we can complain.”
Mark Cavendish won a sprint finish to claim his first National Road Race Championship in Glasgow. The Manx rider overtook David Millar on the home straight and held off the challenge of Ian Stannard, who recovered from a puncture in the penultimate lap to claim silver.
Millar had attacked in the final stages after a four-man leading group had emerged in the ninth of 14 laps of the circuit around Glasgow’s city centre and west end.
But the Scot could not get far enough ahead of Cavendish to negate the Omega Pharma Quickstep rider’s famed sprinting ability.
Peter Kennaugh missed out on a medal after falling behind in the very late stages before the finish in Glasgow Green.
Hull rider David Shackleton had to settle for third spot in The Pete’s Race near Pontefract yesterday, as Lancashire-based riders launched successful forays over the border to take victory.
Riding for the Herbalife team, Wirral-based 29-year-old Giles Drake took victory after attacking mid-way through the race and staying clear by himself for 50 miles to take a deserved win and add to the victory he secured in the Holme Valley Wheelers stage race two weeks ago.
Shackleton, 32 and riding for Wilson’s Wheels, was part of a small group of riders who went off the front of the bunch in search of Drake, but they left it too late to catch him, and in the sprint for the line Shackleton had to settle for third, with Liverpool’s David McGowan taking second spot.
Elsewhere, Ashley Proctor won the Danum Trophy, staged by Doncaster Wheelers around Sprotborough yesterday.
The Whiston Velo rider took the win in a sprint finish from Langsett Cycles rival James Baillie, while Gareth McGuinness (Energy Cycles) was third.
In time trialling, Yorkshire Road Club’s Carl Saint won his own club’s 25-mile time trial on the Topcliffe to South Kilvington course on Sunday. The Slaithwaite rider covered the distance in 53-36 to win by almost a minute from GS Metro rival Andy Fuller, while Mike Marshall (Dirt Wheels Cycles) was third.
Former champion Cadel Evans and emerging talent Tejay van Garderen will lead BMC Racing at the Tour de France, the team confirmed yesterday.
The 36-year-old Evans, who won the race in 2011 and challenged Sir Bradley Wiggins in the second week of last year’s event before falling away, will be contesting his ninth Tour de France.