Sakura beats Lee and anyone can see that. Sakura at Mid-High Chunin level was getting praised by Sasori, a Kage level ninja, for her skills. Chiyo who seen many strong ninjas since Tobirama was alive even praised her. Sakura was trained to analyze and evade, that was pretty much the first combat thing she learned from Tsunade. Sakura doesn't have to see Lee, she didn't see where Kakashi was hiding in the bell test and as a result she punched the ground and found him.
She knows speed is one of Lee's strongest asset so how does she hit what she can't catch? Increase her damage range. She simply punches the ground as she did against the mini Juubi's and Lee dies. The sheer damage radius is too big for Lee to escape from, especially when you factor in that she can add more chakra to her fist to increase her power. Lee stated himself that his taijutsu style focus on external damages, Sakura's Yin seal would heal all of that plus internal damage. Sakura uses chakra blades (used to cut Naruto open), poison Kunai, sleeping gas (which she caught Lee in before) and whatever else Shizune and Tsunade taught her.
She can even summon lager slug to heal her as well. Lee using the gates puts stress on his body by tearing his muscles and it usually last until he uses that gate's big move before he collapse of exhaustion; happens to both Lee and Gai. Plus Lee can only go to 6th gate in Shippuden. Heck, you talk about speed but Sakura hit Kaguya who speed upwards to evade Naruro and Sasuke. So it's no reason to doubt that if Lee is going at Sakura in a linear movement (Sasuke says it's easier to read linear movements) then nothing suggest Sakura can't hit him since Kaguya is faster than 8th gate Gai who is faster than Lee.