VILAMOURA, Portugal, Oct 14, 2012 (AFP) - Lowry, lying four shots off the lead going into the closing day at the Oceanico Victoria golf course, produced his moment of magic when his approach landed a foot short of the hole and hopped in for an eagle two.
He eventually signed for a 66 for a 14-under par total of 270.
This was Lowry's second win on the European Tour, his first coming as an amateur in the 2009 Irish Open.
The 26-year-old, only the second player after Spain's Pablo Martin to win on the tour as both an amateur and a professional, said: "I cannot believe this.
"I can't explain how I feel really. It's a dream come true - I'm over the moon.
"Everyone was referring to me as the fella who won the Irish Open as an amateur, but now I've won such a prestigious event I don't know what to say."
Lowry was still three behind at the turn, but then his luck changed with a birdie at the 10th and the eagle at the next.
"I thought then this could be my day and thankfully it is," he said.
"We had a long wait on the 12th tee which was good, I had time to compose myself."
He was one ahead with one to play, but took five on the last after driving into sand.
But Fisher, seeking his first title since his Ryder Cup debut two years ago, was unable to force a sudden death play-off, also finishing with a bogey.
The Briton came in with a 70 to take second, with 2005 US Open champion Michael Campbell of New Zealand one shot further back in third for his highest finish in four years.
Austrian Bernd Wiesberger, the overnight leader, came in fourth, another shot behind after finding water on the 11th and 17th.
Leading and selected fourth round scores of the Portugal Masters at the Oceanico Victoria golf course on Sunday (par 71, GBR/IRL unless stated):
270 - Shane Lowry 67 70 67 66
271 - Ross Fisher 65 67 69 70
272 - Michael Campbell (NZL) 68 69 67 68
273 - Bernd Wiesberger (AUT) 70 65 65 73
274 - Richard Finch 70 68 66 70
276 - Stephen Gallacher 65 70 72 69, Jamie Donaldson 67 71 72 66, Danny Willett 70 69 74 63, George Coetzee (RSA) 69 73 67 67, Henrik Stenson (SWE) 70 70 68 68, Raphael Jacquelin (FRA) 72 70 71 63
277 - Matteo Manassero (ITA) 71 71 70 65, Gonzalo Fdez-Castano (ESP) 68 71 67 71, Lorenzo Gagli (ITA) 72 69 67 69, Scott Jamieson 71 70 68 68
278 - Francesco Molinari (ITA) 71 71 66 70, Robert Jan Derksen (NED) 70 72 70 66, Ricardo Santos (POR) 72 69 72 65, Andrew Dodt (AUS) 72 70 64 72, Simon Khan 72 70 68 68, Lee Slattery 69 70 74 65, Anthony Wall 68 71 68 71, Thorbjorn Olesen (DEN) 69 70 73 66, Keith Horne (RSA) 69 72 67 70, Mark Foster 71 67 67 73, Padraig Harrington 69 67 71 71
279 - George Murray 66 76 65 72, Thomas Aiken (RSA) 68 71 69 71, Peter Whiteford 70 71 67 71, Mikko Ilonen (FIN) 73 69 68 69, Anders Hansen (DEN) 71 70 69 69, Oscar Floren (SWE) 73 68 67 71, Johan Edfors (SWE) 73 65 75 66, Miguel Angel Jimenez (ESP) 69 68 68 74, Pedro Figueiredo (POR) 70 70 70 69, Fredrik Andersson Hed (SWe) 67 69 70 73
Selected
280 - Hennie Otto (RSA) 70 71 69 70, Richard Green (AUS) 70 68 69 73
283 - Rich Beem (USA) 70 72 71 70
285 - Jbe Kruger (RSA) 67 71 77 70, Matthew Zions (AUS) 70 72 70 73
286 - Shaun Micheel (USA) 74 68 69 75