Cardio, specifically HIIT, stimulates thermogenesis. When you body is in a caloric deficit, over time the metabolism slows due to less food being consumed and it is trying to preserve tissue. Cardio negates this effect.
Additionally, cardio oxegenates the blood and helps to shuttle nutrients. This enables for the body to use what is being put in more efficiently.
Personally, I don't use cardio to get lean, I increase my training frequency and IF NEED BE I add in some HIIT to help facilitate greater fat loss. Heavy, intense weight training actually has a greater EPOC effect than cardio...
Keep in mind, your body is either in a cataolic (fat burning) state of anabolic (growth and recovery) state. For fat loss while preserving muscle, you need to balance catabolism with anabolism through nutrient timing, training and cardio.
Additionally, it goes beyond calories in and calories out. You need to look at the foods you are eating, when you are eating, the intensity of training, duration of training, daily activity level, hormones, sleep, stress levels, digestive health, and supplementation.