Tammy Abraham saved new boss Thomas Tuchel from an FA Cup embarrassment by breaking the resistance of brave Barnsley.
The England striker netted his fourth FA Cup goal of the season to earn a quarter final tie against Sheffield United at Stamford Bridge.
It maintained Tuchel's unbeaten start with four wins out of five games.
But the Blues' victory only came after a half time reshuffle, after Valerien Ismael's side squandered two great chances.
Abraham was presented with a tap in by sub Reece James, who broke well into space down the left.
There was a strong hint of offside and without VAR to help Martin Atkinson allowed the goal – TV replays showing he was right to do so.
Earlier Atkinson had made a mistake when Chelsea were wrongly denied a penalty.
A tackle by defender Tony Sibbick cleaned out Abraham in the box and Atkinson wrongly ruled it was clean.
Abraham then conjured some heroic defending himself, heading Michael Sollbauer's volley off the line late in the day, as the Championship side made Tuchel's men work until the very last minute to book a last eight showdown with Sheffield United at Stamford Bridge.
Chelsea turned in a first half as sloppy as Barnsley were brilliant and tenacious, in a disappointing audition for a host of players handed a chance by Tuchel.
The London superstars lacked urgency and fight. But they soon discovered they couldn't just turn up for the win.
Tuchel has cleaned the slate for players who fell out of favour under Frank Lampard, notably handing a start for £71, keeper Kepa Arrizabalaga, explaining: “This is a new start for him, I don't have a history with him.”
It was also a big night for Emerson Palmieri, Kurt Zouma and teenager Billy Gilmour, who all made their first appearances for the German while Christian Pulisic and N'Golo Kante made their first starts, but did nothing to enhance their claims.
The visitors were stifled by Barnsley's early energetic squeeze, and could have conceded two goals.
Ismael took over October and wanted his mid-table Championship youngsters to show they can dream of being Premier League standard. They did for long periods.
Perhaps inspired by losing 6-0 at Stamford Bridge in the Carabao Cup, they pinned Chelsea back with a bold game-plan.
Kepa was forced into action after ten minutes. Highly-rated Alex Mowatt's inswinging cross was flicked by Conor Chapin. Callum Brittain should have buried a free shot on goal but fired at Kepa, who blocked with his legs.
Ismael says they'd need to take their chances, and that was the biggest of the first half and was wasted.
It was a proper examination for Tuchel's men, on a pitch that had been waterlogged and unfit for use on Saturday, against a side holding their own.
Just before half time Brittain was on the end of a well worked short corner to fire a shot that was goal bound. Unfortunately team mate Victor Adeboyejo got in the way and deflected it wide instead of into the goal.
After the break Callum Hudson-Odoi looked livelier and scudded a shot just wide, as both sides went more direct in a fascinating, well-matched tussle, until Abraham struck.
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