Michael Ballack's first of the season, followed by goals from Salomon Kalou, Nicolas Anelka and Frank Lampard, all quality strikes, recovered a replay in which Southend had taken the lead.
Although the score in the end was comfortable and Chelsea were always the team on top, this match will do nothing to quieten down concerns over set-piece defending after near-shambolic scenes allowed the seaside League One outfit to head in a corner after just 15 minutes.
Ballack's leveller fortunately came at a good time, seconds before the half-time whistle, and in the second period Southend only looked like pulling the game back on one occasion as the Premier League Blues sprinted away.
Scolari made three changes from the Old Trafford defeat - Anelka and Kalou in for Drogba and Deco who were not on the bench. Alex replaced Carvalho.
However before the team sheets were even handed in there was minor drama. Referee Chris Foy initially called the game off due to fog that laid low over this corner of Essex all day. Within a minute of the decision being announced, the mist began to lift and at 7pm, just quarter-of-an-hour later, it had all but gone.
The ref did the sensible thing and reversed the decision. The gates opened on an traditionally tight, lower league stadium.
On two minutes, Kalou made a promising incision through the right of the home side's defence but rolling the ball across the box, he couldn't pick out a team-mate.
Joe Cole on the other side then played a one-two with Lampard but saw his shot saved. It had been a settled start.
But then Chelsea had to defend our first corner on 14 minutes, Alex's misplaced long back pass going astray. It was taken short and it took a Cech stretching save to turn it behind.
From the second corner that followed, this time from the right side, Chelsea lined up in the much discussed zonal method. It didn't prevent Southend centre-back Adam Barrett being found unmarked to head past a helpless Cech.
Two minutes later, shocked Chelsea were back up the other end and Southend left-back Herd had to clear off the line from Joe Cole.
On 24 minutes it took a save from the keeper from Lampard's close range volley to keep the lead, Clarke then blocking a follow-up effort from Joe Cole before Ballack shot over from the edge of the area.
Anelka side-stepped a challenge on the edge of the box but his attempted curler was too straight. Chelsea, as could only be expected, were dominating possession but the chances were hardly clear cut. At least no more set pieces were being conceded!
'It so foggy, call it off!' sung the Chelsea fans.
Ballack came close to improving the mood after combing with Anelka but his 15-yard shot was deflected wide.
He was further off-target and further out when volleying over from a keeper's punch-out on 33 minutes.
Five minutes later Chelsea could easily have gone two down, a deficit from which there would have been big doubts over a comeback.
Former Chelsea man Anthony Grant beat Ashley Cole, was fouled by Mikel (who would be booked for the challenge and now will serve a suspension against Ipswich in the next round) but the ball broke for Sankofa to cross, Cech saving brilliantly low down from Revell's thumping header.
In the two minutes before break, Southend twice tackled Anelka in the box as shooting chances materialised but then came the relief. Mildenhall punched out a Bosingwa cross as he collided with his own defender but only to Ballack. From 12 yards the German finally found the target, half-volleying expertly into the top corner.
There was a half-time change by Scolari, Belletti a straight swap for Mikel as holding midfielder.
The game restarted in the manner it had paused, with Ballack shooting, this time over as he was challenged. Mildenhall then saved well from Ashley Cole.
Alex went close with a header from a Lampard cross as Chelsea impressed in the early minutes of the second half.
The Brazilian soon did well at the other end to marshal Barnard away from goal after the striker had gone round Cech. From the corner that followed, this time Chelsea cleared.
From the next one however, Christophe was free to head narrowly over. Still the defensive system was creaking away.
Fortunately, Salomon Kalou had the class at the other end to make a difference. Found by a superb Joe Cole pass through the defence, the Ivorian went outside Herd before shooting low across the keeper and inside the far post. A 2-1 lead at last with 59 minutes gone.
All was not plain sailing from then on in. Joe Cole was lost to injury, hobbling off having collapsed in pain, seconds after treatment following a Grant foul.
On 77 minutes, Anelka side-footed his team to security as Chelsea outmanoeuvred a tiring Southend - Lampard and the increasingly influential Kalou, from wide out, playing the final passes.
Seconds after the stoppage time board was raised, Lampard and Kalou were again doing damage, the vice captain passing wide and then taking a return to scoop into the net from 12 yards out.
Chelsea will play Ipswich in round four on Saturday 24 January,
Chelsea Cech; Bosingwa, Alex, Terry (c), A Cole; Ballack, Mikel (Belletti h-t), Lampard; J Cole (Di Santo 75), Anelka, Kalou.
Scorers Ballack 44, Kalou 59, Anelka 77, Lampard 90+1.
Booked Mikel 37
Southend (4-1-3-2): Mildenhall; Sankofa, Clarke, Barrett (c), Herd; Christophe; Grant (Francis 79), Moussa, Stanislas; Revell (Betsy 85), Barnard (Freedman 72).
Scorer Barrett 15.






















