The Orica-GreenEDGE rider, who also claimed the Trofeo Campos on Monday, edged out Maarten Wynants (Blanco) and Davide Cimolai (Lampre-Merida) on the last of four days of racing on the Spanish island.
It was a bad day for Team Sky's Ben Swift, though, after the 25-year-old crashed on a descent and was taken to hospital.
Bradley Wiggins also failed to finish, having pulled up after less than 50km.
The day saw the peloton ride a 170km route that started and finished in Alcudia and took in ascents of four category-two climbs, including the Coll de Puig Major.
Ten riders made an early breakaway, but after being caught by a chase group, their ranks swelled to 13.
Team Sky's Xabier Zandio was first over the Puig Major and led the escapees down the steep run to the start of the climb of the Coll de Soller.
The peloton followed around a minute-and-a-half later, but the technical descent caught out Swift, who hit the deck and was later taken to hospital for a precautionary scan.
As the breakaway's gap started to tumble, Angel Madrazo (Movistar) and Robert Gesink (Blanco) made a fresh bid to stay clear, with the Gesink being the final man to be caught after a spirited fight.
That left the door open for the sprinters and Howard once again showed his strong early-season form to claim a second victory in three days.