Charlotte, from Minchinhampton in Gloucestershire, birdied three of the last six holes and finally took the title in a dramatic swing of fortune on the last green.
With six holes to play, Charlotte was three shots behind long-time leader Leona Maguire, one half of the 16-year-old talented Irish twins.
Charlotte, the 2010 England order of merit winner, birdied the 13th, 15th and 16th holes to be one shot behind Leona with two to play.
Both parred the short 17th before Leona, who had made all the running from the start of the 54-hole tournament, ran up a double bogey six at the last, taking three shots to get on the green and a further three putts from six feet. Charlotte had a cast-iron par four for a two-shot winning swing.
"I'm speechless," said Charlotte. "I had no thoughts of catching Leona, even though I was only one shot behind her at the start of the last round. When I bogeyed the ninth, I was only really playing for second or third place and, giving it a go instead of holding back, I started to birdie holes.
"Even when I holed out for a par on the last green, I really didn't think it was to win the Helen Holm. It was only when Leona eventually missed a 2ft second putt, that I realised I had won.
"It's the biggest golf title I've ever won, but I have to feel sorry for Leona."
Charlotte hopes she won't be able to defend the title at Troon next April. "I'm going back to the Tour School later in the season. I failed to get my card last year but I'm not letting that put me off. So I hope to be a tour pro by this time next year although it would have been nice to defend the Helen Holm.
"This was third time very lucky for me. I finished fifth on my debut two years ago and tenth when I came to Troon last year."
Curtis Cup player Holly Clyburn (Woodhall Spa) climbed the leaderboard with a final round of five-under par 70 to share third place. Holly, who birdied the last four holes, said she planned to stay amateur so that she can play in the Curtis Cup match at Nairn in 2012.
Leona Maguire, who was the Helen Holm winner two years ago and won the Portuguese title in January, was the winner of the Under-18s trophy. With her twin, Lisa, she won the team event for Ireland with a total of 437 - six ahead of runners-up England with Scotland third on 446.
FINAL TOTALS
First two rounds over Troon Portland; last round Royal Troon
Par 225 (3x75). CSS 76 76 77
213 Charlotte Ellis (Minchinhampton) 73 69 71.
214 Leona Maguire (Slieve Russell) 69 72 73.
217 Holly Clyburn (Woodhall Spa) 74 73 70, Louise Kenney (Pitreavie) 71 71 75
219 Eilidh Briggs (Kilmacolm) 75 74 70.
220 Pamela Pretswell (Bothwell Castle) 73 76 71, Lisa Ball (Matfen Hall) 72 73 75, Rachael Goodall (Heswall) 72 73 75.
221 Emma Brown (Malton and Norton) 72 77 72, Meghan MacLaren (Wellingborough) 74 74 73
222 Jane Turner (Craigielaw) 75 75 72, Katharina Soehnlein (Germany) 73 73 76, Charlene Reid (Royal Portrush) 74 72 76, Bronte Law (Bramhall) 74 71 77.
223 Emelie Ferlin (Sweden) 74 74 75, Lisa Maguire (Slieve Russell) 73 72 78.
224 Nina Holleder (Germany) 76 71 77, Danielle McVeigh (Royal Co Down Ladies) 74 72 78.
225 Fanny Cnops (Belgium) 80 73 72.
226 Kelly Tidy (Royal Birkdale) 79 73 74, Gillian O'Leary (Cork) 71 78 77, Kelsey MacDonald (Nairn Dunbar) 73 75 78, Samantha Birks (Wolstanton) 75 73 78.
227 Mireia Prat Caballeria (Spain) 76 76 75, Alyson McKechin (Elderslie) 71 76 80, Jessica Meek (Carnoustie Ladies) 72 71`84.
228 Amy Boulden (Maesdu) 78 77 73, Chloe Leurquin (Belgium) 74 75 79, Hannah Grant (Enmore) 75 73 80.
229 Louise Kristersson (Sweden) 77 78 74, Valerie Sternebeck (Germany) 74 76 79, Hannah Barwood (Knowle) 74 76 79, Clara Young (North Berwick) 76 74 79..
230 Denise Kalek (Germany) 82 74 74, Jessica Bradley (Tiverton) 74 80 76, Charley Hull (Woburn) 75 79 76, Jerry Lawrence (Rochester and Cobham) 76 78 76, Rachael McQueen (Troon Ladies) 74 76 80, Becky Harries (Haverfordwest) 76 75 79, Rachael Watton (Mortonhall) 78 73 79, Jess Wilcox (Blankney) 74 76 80, Lucy Williams (Mid Herts) 74 75 81231 Olivia Winning (Rotherham) 77 75 79, Joelle Van Baarle (Belgium) 77 74 80.
232 Claire Smith (Silsden) 81 73 78.
233 Ailsa Summers (Carnoustie Ladies) 79 79 75, Vicki Troeltsch (Germany) 76 81 76, Anjelika Hammar (Sweden) 77 80 76, Emma O'Driscoll (Ballybunion) 73 82 78, Bethany Garton (Royal Lytham) 73 80 80, Shelby Smart (Knowle) 74 78 81, Nikki Foster (Pleasington) 75 76 82.
234 Lauren Whyte (St Regulus) 77 79 78.
235 Charlotte Wild (Mere) 76 79 80.
236 Lesley Atkins (Gullane) 79 79 78, Harriet Key (South Herts) 81 77 78, Daisy Dyer (Chigwell) 76 77 83.
237 Emma Sheffield (Newark) 74 83 80, Ellie Robinson (Middlesbrough) 78 74 75
238 Stephanie Fransolet (Belgium) 76 81 81, Lucy Gould (Bargoed) 80 75 83, Bronwyn Davies (Trentham) 79 75 84.
239 Rebecca Wilson (Grange) 79 79 81, Louise Mernagh (Woodenbridge) 76 81 82, Rebecca McGeehan (Germany) 78 76 85.
240 Cara Gruber (Royal Dornoch) 76 81 83.
241 Rebecca Wood (Hallamshire) 75 82 84.
242 Mariell Bruun (Norway) 79 79 84, Sara Garbutt (Ganton) 79 79 84, Victoria Bradshaw (Bangor) 84 72 86
244 Aedin Murphy (Carlow) 77 77 90.
