The great Egyptian was three times within one blow of going two games down against the gifted Frenchman before Gaultier, overcome with emotion, suffered an injury to give Shabana a 6-11, 13-11, 4-0 victory.
Within five minutes of being on the verge of a commanding lead, the former world number one from Aix-en-Provence found himself with another bitter World Open near miss.
Gaultier put his hand to his forehead, smashed his racket, and squatted on the court in a crumpled heap until Shabana hugged him, picked him up, and helped him from the court.
"Squash players have to be among the best athletes in the whole of sport. It's a damned shame and my heart goes out to him," said Shabana generously of an opponent who held five match points in the 2006 final.
It maintained Shabana's hopes of a fifth World Open title, although the champion deserved plaudits for his comeback from 6-9 and 8-10 in the second game when a brilliant flowering of his strokeplaying talents emerged from the soil of his accurate and disciplined rallying.
Shabana also managed to block out the distraction of Gaultier's confrontations with referee John Massarella.
Several times Gaultier left the court to contest decisions, once the Frenchman asked the Englishman to tell stewards to control wandering spectators, and once Massarella threatened him with a code-of-conduct penalty if he did not return to court.
Gaultier first seemed in trouble at 1-0 in the third game when he took a three-minute injury break for what looked like a hip-and-groin problem. It was three points later, as he ran for a Shabana drop in the top right corner, that he pulled up short, clutching his thigh.
It was the fourth time in the last eight meetings with Shabana that Gaultier had failed to finish the match through injury.
Remarkably, an hour later, something similar happened to Karim Darwish.
The former world number one from Egypt performed the splits trying to retrieve from a back corner and was forced to retire in the third game against Peter Barker, the eighth-seeded Englishman.
Darwish became the World Open's fourth retirement with a hamstring injury. Ramy Ashour, the world number one from Egypt, and Adrian Grant, the world number 14 from England, suffered similar fates in the second round.
Egyptian rising star Mohamed El Shorbagy lost to James Willstrop 3-0 (11-9, 11-8, 11-8).