This may sound too easy, but when my knee begins to hurt, it's time to get new shoes.
How old is the pair you're wearing?
Unless you have problems with the way your legs are natually positioned and the way your feet align new shoes won't help.
The tendons in your knee has been stretched resulting in knee tendinitis.
Best thing you can do is rest it, apply some ice to it now and again. Aspirin/ibuprofen works wonders on knee tendinitis, it'll make you feel like you can do higher intensity cardio again, but I highly suggest against this until your knee is totally painless without taking the aspirin/ibuprofen.