The Irishman went into the final day in Vilamoura trailing overnight leaders Anders Hansen and Mikko Korhonen by a shot, but it was defending champion Andy Sullivan who emerged as his nearest challenger.
Sullivan won the event by nine shots last season and made a big charge once again, picking up birdies on four of his first five holes on his way to a 22-under-par total.
Harrington found himself three shots off the lead at one point, but after turning in 33, a holed bunker shot on the 11th sparked a run of three birdies in four holes to move him ahead.
Sullivan joined him at the summit with a birdie on the 17th, but Harrington matched him on the par-5 and held his nerve down the last after getting a fortunate bounce off a spectator gallery. The win is Harrington’s 15th on the European Tour and his first since he won his third major at the US PGA Championship in 2008. His last win on the PGA Tour came at the Honda Classic in March last year.
“I haven’t won yet this year, so I know the year is nearly done, it’s always important to get a win every year, a winning year,” he said. “It’s a big win. Portugal Masters is a big tournament. I’ve been coming here for 10 years so I’ve always liked it down here. I’ve always liked coming down to Portugal.
“I tried to be really aggressive. The golf course suited me and I just tried to go after every pin I could and make birdies. I have a pretty good short game that was on form this week.”
Semi-retired Dane Anders Hansen and Finn Mikko Korhonen were tied for third at 21 under, with English duo Robert Rock and Chris Paisley, and Scot Paul Lawrie in the group a further shot back.
This was the final week for players to get into the top 110 in the Race to Dubai and Woodsome Hall’s Chris Hanson – in his first full season on tour – has done so in 109th place.
He carded rounds of 68 68 74 66 to place 65th, earning €4,600 for the week to boost his season’s total to €253,254.