A back-and-forth battle saw both men enjoy spells of success, with each of the five rounds difficult to score.
Edgar enjoyed his best moment of the fight in the second round, dropping Henderson with a fierce right hand and following up with a choke attempt.
Henderson fought back, and in similar fashion to the pair's first fight opened up a deep cut on Edgar to keep the bout close.
After five exciting rounds the judges were faced with a difficult decision, giving Henderson the nod by split decision on a scorecard reading 46-49, 48-47, 48-47.
Henderson is now set to face number one contender Nate Diaz in his second defence of the belt late in 2012.