Ramires had fired the Blues ahead in the 25th minute – and the Londoners looked to be in control when they were awarded the spot-kick before the break after Thomas Buffel blatantly handled Florent Maloudaâ€™s attempted cross into the box.
However, the Brazilianâ€™s penalty was saved well by Genk goalkeeper Laszlo Koteles as he dived low to his right – and Jelle Vossen made the visitors pay the price with his 61st-minute equaliser.
It was a disappointing night for AndrÃ© Villas-Boas as his self-confessed â€œdisastrous weekâ€ continued with the Blues’ failure to kill off a game that they should really have won.
“We had fantastic opportunities to win the game but it just didn’t happen,â€ said Villas-Boas.
“One day we will get back to the momentum we had before QPR but at the moment it’s not happening for us.â€
Genk started the game brightly but lacked a real attacking threat in the Chelsea box and it was not long before the visitors, with five changes from Saturdayâ€™s team, started to create a few chances for themselves.
Ramires finally broke the deadlock for Chelsea in the 25th minute, making a driving run towards the box and playing a one-two with Fernando Torres, who chipped the return pass over the Genk defensive line for the Brazilian midfielder to collect and drive across the face of the goal into the net.
The goal brought Chelsea to life and they twice almost doubled their lead from long-range shots. Torres drove his shot wide of the right-hand post and Raul Meireles saw his perfectly hit strike cannon back of the crossbar, inches away from being a spectacular goal.
Genk conceded the penalty soon after, however Chelseaâ€™s failure to take advantage meant the Belgians ended the half with a bit of momentum and they started the second period positively.
An excellent attacking move ended with a rather tame shot from Kevin De Bruyne and Petr Cech also saved well from Kennedy Nwanganga to keep his team ahead.
The home side then started to put Chelsea under a bit of pressure and there was a certain inevitability about their equaliser as De Bruyne linked up well with Fabien Camus, whose cut-back into the six-yard box from the left found Vossen, who stroked the ball into the net first time.
Chelsea brought on Daniel Sturridge, Frank Lampard and Juan Mata in an attempt to win the game but the visitors could not finish their chances.
Meireles picked out Maloudaâ€™s perfect cross but could only head the ball straight at LÃ¡szlÃ³ KÃ¶teles and Sturridge saw an excellent long-range effort tipped over the bar.
However, Lampard spurned the best opportunity, somehow failing to direct a Sturridge cross into the goal from less than three yards out.
Genk very nearly conceded an own goal in the dying minutes when a frantic goal-line clearance by Camus hit team-mate Nadson, but the luck was with the home side and the ball fell wide of the goal and they hung on to claim a point.
Genk: LÃ¡szlÃ³ KÃ¶teles, Nadson, Anele Ngongca, Thomas Buffel (Dugary Ndabashinze, 69), Daniel TÃ¶zsÃ©r, Fabien Camus, Anthony Vanden Borre, Kevin De Bruyne, Khaleem Hyland, Jelle Vossen (Elianiv Barda, 87), Kennedy Nwanganga (Anthony Limbombe Ekango, 82)
Chelsea: Petr Cech, JosÃ© Bosingwa, David Luiz, Branislav Ivanovic, Ashley Cole, Raul Meireles, Florent Malouda, Oriol Romeu (Juan Mata, 77), Ramires (Frank Lampard, 66), Nicolas Anelka (Daniel Sturridge, 66), Fernando Torres
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