Yeah, that could do it. How long has it been since you used the alcohol? Did you pour the alcohol on the outside, or try to use it inside?
What kind of pain are you experiencing? Does it hurt when you pee? Does it just generally ache? Something else?
A note for you for the future - using alcohol (or anything else) on your penis after sex won't get rid of an STD if you've been exposed. If you've been infected, you've been infected and any cleanser or industrial agent or whatever isn't going to change that.