Former Yorkshire champion Morris had battled her way back from four shots adrift in the final round and birdied the last two holes – all to no avail.
But her rounds of 72 73 73 72 meant she has placed runner-up in both English women’s championships this season.
Morris had shared the halfway lead with Giles, whose victory gives her a second national title following her success in last year’s English Mid-amateur championship.
Giles held a two-shot lead after the third round meaning the afternoon turned into a match play situation.
Morris slipped four shots adrift after six holes, but while Giles bogeyed nine and 10, Morris birdied the latter to pull within one.
Giles responded and when she birdied the 14th was three ahead, but Yorkshirewoman Morris parred the 15th, which Giles bogeyed, and birdied the long 17th to be just one behind.
On the 18th, a par-5, both players were just short of the green in two. Giles slightly mis-hit her pitch and it pulled up 15ft short, while Morris played a shot of great finesse which finished about 3ft away.
Giles ignored the pressure to slot home the putt to thwart Morris, who had amassed 14 birdies over the four rounds.
Hallamshire’s Holly Morgan tied 16th (76 79 73 75), while Selby’s Ellie Goodall was tied 22nd (74 74 78 79) having struck two double bogeys in the first four holes of her closing round.
Rotherham’s Olivia Winning (76 75 78 80) shared 27th place, finishing both her morning and afternoon rounds on the final day with birdies at both 17 and 18.
Huddersfield’s Megan Lockett continued her progression in the right direction when she added a third round 73 to the 81 and 76 she had carded previously.
But she closed with a round which matched her first of 81 and slipped back to a still creditable 30th place.