After agreeing to a larger deal last month, Napoli took a physical, which turned up a problem with his hip. Boston withdrew that offer and started working on a new one.
The new deal includes the possibility of bonuses that could raise Napoli's 2013 income to $13 million.
Napoli hit .227 with 24 homers and 56 RBIs last season. He played for the Angels from 2006 through 2010.