Mourinho's first return to the Blues after his December 2015 sacking ended in a humiliating 4-0 thrashing and United ultimately fared little better in this quarter-final capitulation, secured by Kante's stunning strike.
A defensive line-up was expected from United amid pre-match reports of a shortage of strikers, but Marcus Rashford defied illness to start as Mourinho changed his system to match that which Antonio Conte has dominated the Premier League with, and one that the former Blues boss has been far from complimentary about in public.
Mourinho's plans were thrown out of kilter as Ander Herrera picked up two first-half bookings for fouls on the superb Eden Hazard, and Kante - scorer of Chelsea's fourth against United in October - lashed home to give the hosts the advantage.
Without the inspirational Zlatan Ibrahimovic, a depleted United mustered little by way of response as Chelsea suffocated the game with long spells of possession which flew in the face of Mourinho's pre-match jibes about their perceived counter-attacking style which is set to secure Premier League glory.
Chelsea - who threatened a second late on through substitute Cesc Fabregas - join Manchester City, Arsenal and Tottenham in a star-studded semi-final line-up, but this one-sided victory should serve as a warning of the Blues vast double-winning potential.
The inclusion of Rashford was not Mourinho's only surprise as he fielded a three-man defence in an attempt to stifle Chelsea's electric forward line.
And Hazard jolted the game to life in the 16th minute, spinning away from Chris Smalling on halfway and surging into the box before forcing David de Gea into a plunging save, with the Spain international brought into more reflex work by Gary Cahill from the resulting corner.
Herrera collected his first booking when he bodychecked Hazard and the Belgian remained fundamental when he again breached United's backline, but his aim was well off.
However, Hazard's nimble feet outfoxed Herrera once more 10 minutes from the interval, a late tackle earning a second yellow card from referee Michael Oliver and drawing heated protestations from United, which sent Conte into a guard-dog eyeballing of Mourinho as the Portuguese berated the official from the touchline.
United were aghast as Diego Costa went unpunished for a sly elbow into De Gea's midriff, but they clung on to the break, with Marouane Fellaini helping clog up midfield after replacing Henrikh Mkhitaryan.
There was a yawning gap in United's midfield as Chelsea took the lead, however, Kante drifting off Paul Pogba to rip a brilliant shot across De Gea and into the bottom-left corner.
