Chelsea threw away two points when substitute Salomon Kalou gifted Valencia a penalty five minutes from time with a needless handball.
After a dull first half, Fernando Torres and Ramires were denied by good saves from keeper Diego Alves.
Frank Lampard then scored with a smart finish from the edge of the box after a cut-back from Florent Malouda.
But, after the error by Lampard's replacement Kalou, Roberto Soldado converted the penalty.
It was no less than Valencia deserved after dominating possession in the final 20 minutes although Chelsea defended resolutely and restricted the Spanish side to shooting from long range.
Lampard had been recalled to the Chelsea starting line-up while £23.5m signing Juan Mata started against his old club just over a month after leaving.
The visitors started brightly and had an early chance when Valencia's experienced captain David Albeda gifted the ball to Fernando Torres, but the striker was caught by defender Adil Rami as he threatened to shoot.
The home side got themselves in a mess again after 12 minutes when Victor Ruiz pulled down Ramires just outside the box. Lampard drilled a low free-kick past the wall but Diego Alves was down quickly to turn the ball away.
GROUP E RESULT
In the other Champions League Group E match Bayer Leverkusen beat Genk 2-0.
Valencia threatened sporadically in the first half with Miguel having a decent effort deflected wide by Ashley Cole, while Jordi Alba's near-post cross was flicked into the sidenetting by Pablo Hernandez.
The game exploded into life at the start of the second half.
Torres went close shortly after the restart when he rose above the Valencia defence to get a head on Jose Bosingwa's driven cross, but Alves did well to tip his shot wide.
Valencia quickly broke to the other end and David Luiz scrambled back to clear as Hernandez was about to finish off Rami's cross.
Ramires then fired straight at Alves when clean through before the keeper blocked Torres's shot from point-blank range.
But Alves had no chance in the 56th minute when Malouda picked out Lampard to drill home from 20 yards.
The home side pushed forward in search of an equaliser and Cech had to be on guard to deny long-range efforts from substitutes Pablo Piatti and Sofiane Feghouli.
Lampard was replaced by Kalou but the substitute immediately gave the ball to Jonas, whose 25-yard curler was tipped wide by Cech.
The Ivorian then inexplicably handled the resultant corner and referee Nicola Rizzoli had no hesitation pointing to the spot.
Soldado stroked the penalty beyond Cech to deny Chelsea back-to-back victories.
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