The Boels-Dolmans rider added to her Tour de Yorkshire title in April as she caught Barker (Matrix Pro Cycling) with fewer than two kilometres remaining of the 103.7km course.
Barker led by a minute at one stage before being reeled in, with Katie Archibald (Team WNT) and defending champion Hannah Barnes (Canyon-SRAM) finishing second and third respectively.
Deignan said: “It’s great to be in the (national champion’s) jersey again. It’s always such a difficult race to win – you don’t just need good legs, you need a lot of luck too.
“It’s one of the hardest national championships I’ve ever won. I’m very proud of the fact that we have so many women now who are capable of competing internationally as well as domestically.”
Steve Cummings became the first man in a decade to do the time trial and road race double on the Isle of Man.
Cummings followed Thursday’s time trial win with victory in yesterday’s men’s race, catching a breakaway group consisting of Ian Bibby (JLT Condor), Ben Swift (UAE Team Emirates), Peter Kennaugh (Team Sky) and Chris Lawless (Axeon Hagens Berman CT) before staging a late solo attack to cross the line first.
The double had not been done since David Millar achieved the feat in 2007.
Cummings, who only returned to competitive action last week following injury, said: “It was a really tough race, but that style of competition is what you miss when you haven’t been racing – it was punchy and explosive and there were so many efforts.
“I’m back now so we can forget about the injuries. It’s nice to be back doing what I do and looking forward to whatever is next. It’ll be nice to be at the Tour and to get stuck in.”
Mark Cavendish, stepping up his bid for Tour de France selection, finished 21st on his home island.