Go to /usr/share/themes, find the chosen theme (like "Mint Y", for example) and open
/cinnamon/cinnamon.css file with any text editor. Since you're in /usr, you'll have to open it with sudo. In that file find this:
The numbers won't be the same as these. These numbers are for my panel: black with 40% opacity (60% transparency). The numbers in the brackets basically mean this: Red, Green, Blue, Alpha Color. "Alpha Color" stands for opacity. You can use a program like KColorChooser to test RGB combinations and see which one suits you.
After editing the color to the desired levels, I recommend you to copy the edited theme to ~/.themes (also change its name, so you can find it easier after editing) and change settings for the system to use the theme from ~/.themes. Local user settings take priority over what's in root.