The FA WSL Player of the Year poked the ball home from close range after 37 minutes to successfully cap a period of Chelsea supremacy.
Emma Hayes’s side had chances to win The Final by a more comfortable scoreline, most notably through Gemma Davison and player of the match Eniola Aluko.
But the one goal was enough for the Blues to secure their first ever piece of silverware in front of a record Final crowd of 30,710.
It was the first time this showpiece match was staged at Wembley and it rounded off a fine summer for women’s football, following England’s historic third-place finish at the World Cup in Canada.
After a quiet start the London club began to carry the greater threat – and they got stronger as the first half went on.
Davison looked sharp on the right, but was unable to produce a telling final ball on a consistent basis.
Her best pass of the first half, a beautiful through ball between Alex Greenwood and Amy Turner, fell into Aluko’s path – but after rounding the on-rushing Carly Telford, the England striker hit her shot into the side netting from a tight angle.
The increasingly influential Aluko, now a three-time Cup winner, came even closer just minutes later when her 18-yard shot was parried away by her international colleague.
The 28-year-old was at the heart of the action once more when she sent over a deep cross to Davison, but the winger somehow contrived to cushion a volley back across goal and wide.
Aluko’s best moment of the half helped Chelsea take the lead. She collected Millie Bright’s pass, advanced into the County box, past Sophie Walton and Turner before feeding Ji six yards out.
The Lady Pies’ first decent effort at goal came on the hour mark when Canada international Desiree Scott had her 20-yard shot deflected behind by Gilly Flaherty.
The resulting corner was headed goalwards by Leanne Crichton and was cleared off the line by Davison.
But back came Chelsea as Aluko saw her low, angled drive turned behind by Telford, who played for the Blues in their 2012 Final defeat by Birmingham.
Last season’s FA WSL 1 runners-up had a great opportunity to kill the game off with 15 minutes remaining but Flaherty could only lift the ball over the bar from a matter of yards.
However, Notts County were unable to punish their opponents and Chelsea held on to secure their maiden SSE Women’s FA Cup crown.
Chelsea (4-3-3): 1 Hedvig Lindahl; 3 Hannah Blundell, 6 Niamh Fahey, 5 Gilly Flaherty, 11 Claire Rafferty; 24 Drew Spence, 4 Millie Bright, 17 Katie Chapman (C); 7 Gemma Davison, 10 Ji So-Yun, 9 Eniola Aluko.
Substitutes: 16 Ana Marques Borges for Aluko 81, 19 Laura Coombs for Ji 90
Substitutes not used: 13 Marie Hourihan, 20 Jodie Brett, 23 Marija Maredinho Banusic
Goal: So-Yun 37
Bookings: Chapman
Manager: Emma Hayes
Notts County (4-3-3): 1 Carly Telford; 14 Sophie Walton, 23 Laura Bassett (C), 15 Amy Turner, 3 Alex Greenwood; 18 Leanne Crichton, 11 Desiree Scott, 4 Danielle Buet; 7 Jess Clarke, 8 Rachel Williams, 9 Ellen White
Substitutes: 2 Dunia Susi for Williams 56, 20 Aileen Whelan for Buet 76, 10 Fiona O’Sullivan for Crichton 83
Substitutes not used: 19 Ashleigh Plumptre, 30 Laura-Jayne O’Neill
Manager: Rick Passmoor
Referee: Amy Fearn
Attendance: 30,710
