I'm not really sure that I understand the question. The answer seems straightforward enough - lower the exposure level. Perhaps the question is how one should go about lowering the exposure level.
If you are shooting in full manual mode, that's as simple as stopping down the aperture, shortening the shutter speed, or reducing the ISO.
With the camera doing the metering, adjusting the ISO, shutter speed, or aperture won't help because the camera will just adjust the other values to get the exposure that it thinks is correct. You need to either overrule the camera's notion of correct exposure or change the way the camera meters the scene.
To override the camera's sense for correct exposure, you can dial in exposure compensation, perhaps to -1/2 stop. Just be sure that you turn off the exposure compensation when you are done or you really will be underexposing shots later.
Adjusting exposure compensation is most useful when shooting a scene that will fool the camera's meter. A common example is shooting scenes with lots of snow. The camera's meter assumes that everything in the world is a lightish shade of gray. When it sees a predominately white scene like someone in the snow, it thinks "wow, that gray is brightly lit" and reduces the exposure to make the snow look gray. Conversely, if you shot someone in front of a lot of black stuff, the camera thinks "wow, that gray is poorly lit" and increases the exposure to make the black look gray.
In your case, it looks like the camera was off because it metered off of the center of the subject. It decided that you wanted the flower to look really good and weren't concerned that the surrounding sky would get blown out. When shooting a backlit subject, it is often difficult for the camera to determine what it should do. If it meters for the subject, the background gets blown out. If it meters for the background, the subject ends up too dark. You can force it to meter off of whatever you want by aiming the center of the lens at your desired subject and pressing the spot-meter button.
Another option would be to use a flash for the shot. That would illuminate your subject so that it is closer in brightness to the background. The camera can only capture so many different light levels (called the dynamic range), so reducing the dynamic range by lightening dark areas with a flash is sometimes the only way to capture everything in a scene.