A superb substitute performance from Adam Le Fondre conjured up an incredible late fightback as the Blues let slip a comfortable lead, putting the manager under pressure.
Juan Mata grabbed the opener, driving home from close range after a superb through pass from Fernando Torres, before Frank Lampard belted a header into the top corner halfway through the second half.
Adam Le Fondre orchestrated the comeback, scoring twice from the bench as the Royals continue their fine unbeaten form.
Brian McDermott had an almost fully-fit squad to choose from and made seven changes from the FA Cup win over Sheffield United. Adam Federici continued in goal in place of Alex McCarthy (shoulder) and Jason Roberts (hip) remained out, with Pavel Pogrebnyak returning to the starting lineup after being rested.
Chelsea, meanwhile, was without Eden Hazard, who is serving his suspension for kicking a ball boy at Swansea, which meant Ryan Bertrand started in midfield for the Blues as Rafael Benitez made two changes from the draw at Brentford, bringing in Cesar Azpilicueta and Mata at the expense of John Terry and Marko Marin.
Ross Turnbull continued in goal with Petr Cech (calf) still injured, while David Luiz (ankle) was also sidelined.
The away side started to control the flow of the game after a turgid start, keeping possession for long periods, but was unable to make a quick impact on the Reading defense. However, Reading forced a couple of free kicks in dangerous areas when Pogrebnyak caused problems for the Chelsea defense, but the Royals were unable to create a decent chance.
Ashley Cole then blasted a long-range effort over the bar, before Torres was shut out by Adrian Mariappa and Federici after a looping ball caused problems for the Reading defense.
Lampard had a shot blocked as Chelsea continued to press, but Torres was penalized later on for clipping Mariappa after the defender sliced a simple clearance.
Gary Cahill wasted a glorious opportunity from a Lampard free kick, failing to connect with the ball when he was unmarked. After the home side cleared another set piece, Jimmy Kebe had a chance to break but was too slow to react as Cole came running in to intercept.
The Chelsea left back blasted another speculative effort way off target after Torres had struck a shot out for a throw, and as the break approached Chelsea didn’t really look like breaking through the Reading back line.
With practically the last kick of the half, however, Chelsea took the lead. Torres collected the ball and scooped a delightful pass into the path of Mata, who fired the ball first time low past Federici.
Torres got in behind the defense early after the break but Reading managed to clear the striker’s cross, with three Chelsea players waiting in the box. Alex Pearce then brought down the Spain international 30 yards out, and Lampard’s belted free kick came straight back off the wall.
Oscar should have made it two when he sprung the offside trap to meet Lampard’s floated ball, but the Brazil international tried an acrobatic finish which flew wide, when he had plenty of time to take a touch in the box.
Oscar was involved again as he was set loose by Lampard, but the midfielder’s cross was cleared by the Reading defense. From the resulting corner, Lampard rose highest to meet Mata’s ball and hammer a header into the top corner.
As the half went on Reading had opportunities from set pieces but failed to work Ross Turnbull. Substitute Adam Le Fondre saw a header fly high over the bar, before the striker curled another effort just over from 20 yards.
Oscar had a chance to make it three late on but was denied by Federici, and at the other end Le Fondre latched on to a through ball to get the home team back in it with a low strike into the near post from the same position as Mata's in the first half.
Ramires then forced a fine stop from Federici 30 yards out, before Le Fondre was there to equalize with a volley deep into the area which flew past Turnbull to set the home crowd into raptures.