The Australian beat Tyler Farrar (Garmin-Sharp) and José Joaquin Rojas (Movistar) in a bunch sprint at the end of a 167km trek from Campos to Ses Salines.
Christian Meier (Orica), Natnael Berhane (Europcar), Amets Txurruka (Caja Rural), Fabio Calabria (Novo Nordisk), Roman Van Zandbeek (De Rijke), Jon Larrinaga (Euskadi) and Luis Mas (Burgos) were involved in an early break.
They built up a lead of over seven minutes as the peloton travelled through the south of the island doing two full laps of a 62km rolling circuit with many small climbs.
But their advantage was down to under three minutes with 65km remaining and they were caught with 27km left to set up a sprint finish where former omnium world champion Howard claimed his first victory on the road since September's Tour of Britain.
“We wanted to be right at the front with two kilometres to go,” Howard explained.
“There were some really nasty corners, and we needed to be at the front when we went around them. Mitch (Docker) and I were fifth and sixth wheel when we hit these corners. It was perfect.
“Then, there were two tight corners with 300 metres to go. I came out third wheel behind Tyler Farrar. It’s great to repay the team for the faith they have put in me for the last two races – especially Mitch.
“We’re working really well together. Like I said during San Luis, we’re still getting used to each other. Three sprints in, and we’ve already won a race. It’s fantastic. He’s done such an awesome job. The whole team has. Hopefully there’s more of this to come.”
Challenge Mallorca sees teams able to enter squads of 10 riders and rotate their line-up through the four days.