What you saw was a concussed fighter just operating on autopilot. The big right hand put JDS's brain on sleep mode and he didn't start to wake up until the 4th round. Not to mention the fact that JDS has had nothing but smooth sailing in the UFC - the guy has basically won every minute of every fight, and it's pretty obvious that he started to believe he was invincible. So I'm sure that getting pounded like he did in the first had his head reeling (concussion aside), and he was lost and confused. The real test is how he bounces back from this.
JDS won the first fight with a big right hand. Cain took the second with the big right hand. If JDS can win a couple fights in a row in impressive fashion, this sets up quite the trilogy. This has the makings of the most noteworthy and compelling storyline that the UFC heavyweight division has had to date.