The tournament saw the leading 24 after Saturday's third round playing a series of six-hole knockout stroke play games.
Santos remarkably holed from 255 yards for his albatross on 18 to beat Chile's Nico Geyger at the last-16 stage.
But Santos soon exited and 23-year-old Sciot-Siegrist beat Italy's Alessandro Tadini in the final at Galgorm Castle.
The unique format saw the players competing over the 17th, fifth, sixth, seventh, eighth and 18th holes at the Ballymena venue.
University of Louisville graduate Sciot-Siegrist played the six shootout holes in three under par as he birdied both par threes and also the closing hole after two putting from 25 feet following a nerveless approach shot.
The Paris native, whose mother hails from Dublin, was earning his first Challenge Tour triumph as he denied Tadini, 43, a fifth success on Europe's second-tier circuit.
Tadini led after the first hole in the decider after chipping in from off the green but former US collegiate star Sciot-Siegrist bossed the remaining five holes as he fired to within eight feet on both the par threes.
"It's amazing," said the 23-year-old Frenchman.
"It's my first full season as a pro so I am so happy because I've been working really hard this winter and holding this trophy, I don't know how to describe it, it's just pure joy."
Not surprisingly, Sciot-Siegrist lauded the event's format which was a slight tweaking of the final-day match play format used at the Perth World Sixes in Australia earlier this year.
"It's great to change the format from what we usually play and I really enjoyed it."
Sciot-Siegrist, who was ranked as the world's 22nd best amateur, had earlier looked set to bow out against England's Tom Murray at the last-16 stage before an eagle three at the last gave him victory.
However, moments later there was astonishing drama at the closing hole as Santos, trailing Geyger by one, took victory in the second-round match as he holed out for his albatross.
However, the Portuguese player then exited at the quarter-final stage against Germany's Christian Braeunig.
That left Braeunig facing Sciot-Siegrist in the last four and after chipping in for eagle from the length of the 18th green to bring the encounter to a play-off, the German looked favourite as he faced a two footer at the first tie hole with the Frenchman eight feet away.
However after Sciot-Siegrist holed, Braeunig's drilled tiddler lipped out to send the Frenchman into the final.
Tadini, who has been back and forth between the European Tour and the Challenge circuit since first earning his main card in 2003, progressed to the decider after beating Scotland's Bradley Neil by four shots in the first semi-final.
Earlier, a closing Tadini eagle in the quarter-finals had ended the hopes of Austria's Matthias Schwab, who had led the 24 qualifiers after the the 54 holes of stroke play.
Santos ended Cormac Sharvin's hopes early on Sunday morning after playing their six-hole match in three under par which left him three strokes ahead of the Ardglass man, the only Irishman to progress to the shootout stage.
Pop star Niall Horan, whose golf management company were centrally involved in the Galgorm Castle event, made the trophy presentation after a week which drew 43,495 spectators to the Ballymena venue.

The 25-year-old has been advertising his club's car sponsor and has also appeared in adverts for petrol.
Reus also received speeding tickets on at least five occasions from 2011 before authorities realised he had been driving without a licence.
"The reasons I did it are something I cannot really understand," he said.
Dortmund said they had discussed the matter with the player and spokesman Sascha Fligge said: "He has promised such a thing will not happen again."
Reus, who missed Germany's World Cup triumph in July after picking up an ankle injury in the final warm-up game, has repeatedly been linked with a move to the Premier League but is currently out until the New Year with another ankle injury.
France's Robin Sciot-Siegrist won the Northern Ireland Open as Portugal's Ricardo Santos carded an albatross on a dramatic shootout Sunday.
[NEXT_CONCEPT]
Borussia Dortmund and Germany winger Marco Reus has been fined more than half a million pounds for driving without a licence.