Petr Cech saw stars after just 15 seconds when he was caught by Steve Hunt's knee and then replacement Carlo Cudicini was knocked cold by Ibrahima Sonko during a frantic finish.
That left skipper John Terry between the sticks for the final two minutes of stoppage time, but Chelsea hung on to take all three points.
The crucial goal came on the stroke of half-time and was a freak strike for the champions. Frank Lampard's free-kick from the edge of the box deflected off Sonko and then hit the hapless Ivar Ingimarsson before rolling beyond the helpless Marcus Hahnemann.
Reading battled bravely for an equaliser and Kevin Doyle hit the post, but both sides had a man sent off in a feisty second half. First, John Obi Mikel saw red for tugging back Sonko to earn a second yellow card.
Then Reading substitute Andre Bikey followed him down the tunnel after he too picked up two yellow cards.
The defeat was Reading's first at home since August 2006, the opening day of their Championship title-winning season.
But Steve Coppell's side will feel unfortunate not to have preserved that unbeaten record after more than holding their own against Jose Mourinho's champions.
Reading gave Hunt his first Premiership start in place of Bobby Convey on the left wing - and the spiky midfielder made an instant, though accidental, impression on goalkeeper Cech as he chased down a long ball.
Cech failed to recover after five minutes of treatment, Cudicini replacing him, as Chelsea were forced into an instant rethink.
And Reading, just as they had in their previous home game against Manchester United, gave them plenty to think about too.
Ingimarsson headed wide from a corner on 12 minutes, the start of an eventful first half for the Icelandic defender. Five minutes later he headed Paulo Ferreira's shot against his own crossbar with Hahnemann stranded in no-man's-land, and the centre-back was then yellow carded for a halfway line trip on Andrei Shevchenko.
And an eventful half came to a dramatic finale for Ingimarsson when Lampard's deflected free-kick bounced off his legs and into the empty net to give Chelsea a freak breakthrough.
Before that, Reading had been desperately unlucky not to take the lead themselves, Doyle spinning and poking a left-foot shot on to Cudicini's post after great work by Hunt down the left.
Reading continued to match their illustrious rivals after the break and were unfortunate not to get back on level terms when Steve Sidwell drove a low shot just wide midway through the second half.
And as frustrations reached boiling point late on, Reading coach Kevin Dillon and Chelsea fitness coach Rui Faria were sent to the stand after a brief scuffle in front of the visitors' dugout.