The two legends had previously met a total of 22 times on the PSA World Tour, with Shabana holding a 13-9 record. The match started out well for the "Prince of Cairo" who took the first game 11-6.
The two former world number ones and world champions traded points back and forth to six-all in both the second and third games - but it was 35-year-old Lincou who applied the pressure from this point forward and was able to secure both games.
With Shabana the victor in their last meeting in the US Open last year, the packed crowd no doubt expected a comeback from the left-hander - and the 32-year-old Egyptian again forced the pace to take the fourth game to six-all.
But strong play from Lincou, and a few unforced errors from Shabana, saw the Frenchman move three points clear. Lincou was able to maintain the pressure to secure his 6-11, 11-8, 11-6, 11-9 upset after 48 minutes.
"I am very pleased," 2010 champion Lincou told event MC Neil Harvey afterwards. ""He's a legend of the game.
"I had to make sure I really pushed him to the back - and not give him any loose balls.
"Some days you are very focussed, and other days not," added the world No12 from Marseille. "But today was a good day for me."
Lincou, the only unseeded player to make the last four, will now take on another Egyptian Hisham Mohd Ashour. The No3 seed from Cairo beat South African Stephen Coppinger 11-8, 11-9, 6-11, 11-6.
England's Daryl Selby had cause for celebration in his clash with Borja Golan when he beat the top-ranked Spaniard for the first time in his career. Indeed, it was only in the pair's fourth meeting that Selby earned his first game against Golan.
But fourth seed Selby, runner-up in 2010, was in the mood for revenge, and despatched his unseeded opponent 11-6, 11-7, 11-7 in 56 minutes to reach his second semi-final in three years.
"Well if only I could play like that every time I stepped on a squash court!" tweeted the world No11 from Chelmsford later. "Very pleased with a 3-0 win against Borja. @ljanjema tomorrow."
RESULTS: PSA International 50 Bluenose Classic, Halifax, Nova Scotia, Canada
Thierry Lincou (FRA) bt  Amr Shabana (EGY) 6-11, 11-8, 11-6, 11-9 (48m)
 Hisham Mohd Ashour (EGY) bt Stephen Coppinger (RSA) 11-8, 11-9, 6-11, 11-6 (52m)
 Daryl Selby (ENG) bt Borja Golan (ESP) 11-6, 11-7, 11-7 (56m)
 Laurens Jan Anjema (NED) bt Julian Illingworth (USA) 11-4, 13-11, 11-7 (38m)
Thierry Lincou (FRA) v  Hisham Mohd Ashour (EGY)
 Laurens Jan Anjema (NED) v  Daryl Selby (ENG)
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