Stannard left breakaway companions Kristian House (One Pro Cycling) and Graham Briggs (JLT Condor) with 40km to go and took advantage of an unenthusiastic chase from the peloton to reach the line first.
The 29-year-old recorded his first win since the 2015 Omloop Het Nieuwsblad, finishing over five-and-a-half minutes ahead of the peloton, with Briggs and House claiming second and third respectively.
The trio were initially joined by Matt Cronshaw (Madison Genesis) in the breakaway, but the Carnforth rider was distanced on the climb of the Britckworks with 65km left.
Stannard, House and Briggs worked well together to increase their lead over the peloton to over six minutes, but with 40km remaining Stannard decided to go it alone.
With the Team Sky man sitting 15 minutes back on race leader Julien Vermote the peloton weren’t too keen on going all out to bring the big man back.
The sprinters’ teams were also unwilling to do the work, with Mark Cavendish (Dimension Data) going on a little sojourn off the front of the slow-moving peloton at one stage to demonstrate just how slow the pace was.
Stannard’s lead only increased as he reached the line in Tatton Park, with Briggs outsprinting House shortly after to seal the all-British podium.
Having shown little hustle all day, the sprinters lined themselves up for the battle for fourth place and some valuable points in the sprint classification in the final kilometres.
Danny van Poppel (Team Sky) and Nicola Ruffoni (Bardiani CSF) had to be separated by a photo finish in the race for fourth, with the Italian getting the nod from the judges.
The peloton faces the longest stage of the race on Wednesday, with a 218km rolling challenge between Denbigh and Builth Wells sure to test the legs once more.
Tour of Britain stage three, Congleton – Tatton Park (179km)
1. Ian Stannard (GBr) Team Sky, 4-14-12
2. Graham Briggs (GBr) JLT Condor, at 1-46
3. Kristian House (GBr) One Pro Cycling, st
4. Nicola Ruffoni (Ita) Bardiani CSF, at 5-43
5. Danny van Poppel (Ned) Team Sky
6. Ramon Sinkeldam (Ned) Giant-Alpecin
7. Chris Latham (GBr) Team Wiggins
8. Rick Zabel (Ger) BMC
9. Dylan van Baarle (Ned) Cannondale-Drapac
10. Luka Mezgec (Slo) Orica-BikeExchange
Overall standings after stage three
1. Julien Vermote (Bel) Etixx-QuickStep in 13-53-15
2. Stephen Cummings (GBr) Dimension Data at 6 secs
3. Daniel Martin (Irl) Etixx-QuickStep at 1-04
4. Ben Swift (GBr) Team Sky at 1-08
5. Xandro Meurisse (Bel) Wanty-Groupe Gobert at 1-08
6. Tony Gallopin (Fra) Lotto-Soudal at 1-08
7. Dylan van Baarle (Ned) Cannondale-Drapac at 1-12
8. Guillaume Martin (Fra) Wanty-Groupe Gobert at 1-12
9. Tom Dumoulin (Ned) Giant-Alpecin at 1-12
10. Nicolas Roche (Irl) Team Sky at 1-16