He's not dead, though. He cut off his own head before he died, and then a month later attacked Jonathan on a boat. He used a technique to make Jonathan unable to breathe, thus blocking the Hamon technique. Jonathan defeated Dio and threw his zombie helper into the steam engine, rigging the boat they were on to explode. Dio attempted to cut off Jonathan's head and replace his head with Dio's, but Jonathan stabbed Dio in the neck and moved him into a position where he couldn't move. There, Jonathan died with Dio in his arms... And after the boat exploded, Dio cut off Jonathan's head and mounted his own on Jonathan's body.