Well, strictly speaking, it was one-sided. They'd been close for three years but Shizuru kept her feelings bottled up inside her out of fear of rejection. So she played the loyal friend while secretly wanting to throw Natsuki down on a bed somewhere and have her way with her. Her true feelings were revealed at the wrong way in the wrong time and emotional wreck Natsuki reacted in exactly the way she feared she would, which drove her over the edge (straw that broke the camel's back, etc.).
Natsuki did love Shizuru even then, but she was too focused on her mother to realize it and too emotionally crippled to really understand it. Even then, she tried to make sure Shizuru understood before ending it. Then they were given a second chance at life and a postscript story assures us that happiness will find them soon.