Diego Costa's fourth goal in three games handed Chelsea the perfect start, only for Guus Hiddink's men to drift off and allow League One side Scunthorpe to turn the tie into a scrap.
The 19-year-old Loftus-Cheek's composed finish secured Chelsea safe passage to the fourth round, though, after Scunthorpe were denied a second-half penalty.
Chelsea will hope England Under-21 star Loftus-Cheek's tidy performance points to a coming of age, after limited past opportunities.
And interim Blues boss Hiddink will be heartened by hit man Costa taking another step forward in his fight for top form
Total first-half control caused Chelsea to switch off and coast to a 1-0 advantage at the break.
Costa sneaked goal-side of the defence to turn home Branislav Ivavonic's cross and hand the hosts the perfect opening.
Oscar curled wide from 16 yards instead of doubling the lead, doing an injustice to his step-over and link return ball from Costa - the pair combining well after their set-to in training this week.
Pedro then spurned another fine Chelsea chance, scuffing his finish after a lose first touch
Willian's smart step-over drew the defence after Fabregas' raking pass set Ivanovic away down the right
Gary Cahill and Cesar Azpilicueta's tangle set Williams tearing away down the right, but Kurt Zouma pulled off the perfect sliding cover tackle to deny the winger a one-on-one.
Suddenly emboldened, Scunthorpe pressed again, only for Kevin Van Neen's cross to evade Neal Bishop.
Hiddink took off Oscar at half-time in favour of youngster Loftus-Cheek, but still the craved impetus failed to arrive.
Chelsea were handed another let-off when referee Craig Pawson denied Scunthorpe a penalty despite Ramires tangling with Van Neen in the box.
Ramires appeared to tread on the Scunthorpe forward's foot, but the appeals went unanswered.
Bishop and Stephen Dawson hounded Costa into losing possesion in his own half, only to be hauled back for a foul on the Spain striker.
Finally Chelsea killed the tie, the long-overdue second goal courtesy of the highly-rated Loftus-Cheek
Ramires broke up play and fed Willian, who set Azpilicueta free on the overlap
Costa's selfless near-post run drew the defence and Loftus-Cheek swept home.
Van Neen dragged a free-kick just wide in a bid to catch Begovic cold at his near post, before Scunthorpe were lucky not to concede a penalty of their own, Loftus-Cheek's progress in the box seemingly stopped by a stray hand.
Jordan Clarke's pile driver shot then forced Begovic into a first-class reaction save to tip onto the angle of post and bar, but by that stage Chelsea were home and hosed.
Source : PA