The 32-year-old headed into the ninth and final round of the season, which acted as the Olympic test event, leading the overall standings by 62 points ahead of Latvian Oskars Melbardis.
Rush was far from in the form that saw him win in La Plagne and Koenigssee earlier in the season but a finish of equal fourth, just 0.65seconds off first, was enough for him to hold onto first place overall.
Hefti took his third victory of the season and second in a row on just his fifth appearance with his late start on the World Cup circuit and following successes aiding Rush’s course.
He beat Germany's Thomas Florschuetz into second by 0.30 while all Melbardis could manage was third a further 0.10 adrift as he ultimately fell 54 points shy of overthrowing Rush.
Rush finished with 1656 points to become the first Canadian since Pierre Lueders in 2006 to win the two-man title and the second this season after Kaillie Humphries' two-woman success on Friday.
Hefti was untouchable in the Olympic host city in Sochi as he clocked the fastest time of both runs, 56.73 and 57.03 with Florschuetz the man behind him on both to place second.
Melbardis clocked the same first-run time as Florschuetz, 56.89, but was slower than him and Hefti with his second run and had to make do with third and second in the overall World Cup standings.
Rush was fourth quickest first time out and then sixth second time out to tie for fourth with Alexander Zubkov while Britain's John Jackson was 16th for his best finish in three rounds.
Pushed by Bruce Tasker in Sochi, Jackson was once again joined by fellow Brit Lamin Deen in the two-man event, who with the help of his previous brakeman Craig Pickering, placed 28th.