Warning! This article contains heavy spoilers on the last arc of Chainsaw Man. It will answer in detail how Denji beat Makima, and give the context and aftermath of their multiple chapter long battle.
Denji beat Makima by sneak attacking her. He suspected she was seeking his heart by scent alone, so Denji temporarily removed it from his chest and used blood he received from a contract with Power to stay alive and hidden until he could strike.
The “Denji” that Makima was fighting was actually just Pochita taking his form. Once Makima ripped Pochita out of the fake Denji’s chest, she grabbed some cigarettes from a fallen devil hunter. She assumes she won.
The real Denji rose from a pile of devil hunter bodies, wearing one of their uniforms to blend in. He walked up from behind her and tore through her middle with a chainsaw infused with Power’s blood for extra internal damage.
Kishibe pulled into the graveyard with a van to pick up Denji and the defeated Makima. Denji cooked Makima’s remains into a soup to ensure her defeat. Some time later, Denji explained his scheme to Kishibe.
“There was something I figured out from my past knowledge and conversations. Makima perceives us through her sense of smell. She doesn’t remember one face from another. Anyone who interests her will only be remembered by her smell, so I took a gamble. A bet that Makima only saw Chainsaw Man this whole time and that she didn’t even notice someone like me.”
Denji to Kishibe | Chapter #97
So that’s the answer. Denji beat Makima by taking advantage of her sense of smell, assuming that she was only able to track Pochita and would not notice Denji if he removed himself from his heart and struck from the shadows.