A combination of an unfamiliar line-up coupled with a determined Scunthorpe United performance resulted in the potential for a cup shock.
And a mini shock came after just eight minutes when the Iron rocked the 40,019 packed into Stamford Bridge with the opening goal.
Didier Drogba made no real effort to close down wide man Matthew Sparrow on the right.
Sparrow twisted Drogba into the ground before curling an excellent left footer into the Chelsea penalty area.
Paul Hayes was the quickest to react and he collected the ball in one move, before turning Alexei Smertin and arrowing a right footer low towards Carlo Cudicini.
The Italian goalkeeper could do nothing as the strength of the shot beat him and went through his legs into the net.
The 6,000 Scunthorpe faithful went delirious with excitement as the ramifications of the goal sunk in.
For Chelsea, it meant they had to start showing why they are top of the Premiership.
But with debutants Steve Watt and Nuno Morais in defence alongside makeshift centre-back Smertin, not conceding a second goal was a priority.
Eventually, Chelsea'a ability to retain possession counted and on 26 minutes they got their reward.
Eidur Gudjohnsen chipped the ball into the penalty area and it fell invitingly to Mateja Kezman.
The Serbian striker dispatched a beautifully executed right-footed volley that, with the help of a slight deflection, sailed into the net past the helpless Paul Musselwhite.
The relief was palpable among the Chelsea players but still Scunthrope did not give up.
Two minutes after the equaliser, Cudicini was forced into an excellent save diving low to his left to parry a powerful Andy Butler header away from goal.
Then a minute from the break a quick counter attack by the Blues saw Kezman get a foot to a return pass from Drogba. Unfortunately for the striker, he screwed the ball wide of the goal.
Chelsea will need luck to win the FA Cup this season, and perhaps it came on 58 minutes when they took the lead.
A Tiago ball to Drogba saw the Ivory Coast man take the ball into the penalty area and his left footed cross was deflected off the boot of skipper Andy Crosby into his own goal.
It was not what battling Scunthorpe deserved and substitute Cleveland Talyor had two excellent chances to equalise.
His first on 73 minutes resulted in a excellent save by Cudicini, the second six minutes later saw his flicked header rebound off the Chelsea stopper's left upright.
With five minutes remaining, substitute Arjen Robben went on a mazy run. His shot was saved by Musselwhite who then blocked the rebound shot by Cole.
However, the third shot fell to Gudjohnsen, free on the six yard line, and he slammed the ball home.
The scoreline was rough justice on the League Two leaders, but Chelsea are through and the dream of four trophies this season lives on.
MAN OF THE MATCH: Peter Beagrie (Scunthorpe) The veteran winger still has enough skill to compete at the top level and was a constant thorn in the side of Chelsea's unfamiliar rearguard.