The Etixx-QuickStep rider edged out Juan Jose Lobato (Movistar) and Australian team-mate Mark Renshaw respectively to claim victory in the 185.9km race in the southern Spanish region of Andalusia in a time of 4hr 36min 19sec.
Cavendish won two stages on his way to overall victory at the Tour of Dubai last week and an earlier stage victory at the Tour de San Luis in January, giving him four for the season to date.
He racked up 14 victories in 2014, in what for him was a disappointing season but he appears close to his best again in winning the races he should, so far in 2015.
The Almeria victory now puts Cavendish squarely in the middle of the favourites picture for Milan-San Remo (MSR), a race he'd love to again win.
He'll line up for the near 300km 22 March classic along with many of the world's best roleurs and sprinters, on a course that this year is well suited to a fast finisher.
There the competition will be deep, and he has won before, in 2009.
And while his fast start to the season marks him as a favourite there is at least one rider breathing over his shoulder, Katusha's Alexander Kristoff.
Kristoff is the defending Milan-San Remo champion and he also got his season off to fast start at the windswept Tour of Qatar, scoring three sprint victories.
Kristoff had a breakthrough 2014 with a combined 17 stage victories and classifications, including two big stages at the Tour de France to match MSR.
Given his rising status and MSR victory last year, Kristoff will head into the race as the favourite, but as each day passes its clear that Cavendish will be in the mix.
SBS will broadcast Milan-San Remo LIVE on Sunday 22 March from 2345-0300 on SBS ONE (Live Eastern States/SA) with streaming online here at Cycling Central.