Gislason turned in the winner after Cesar Santin, who opened the scoring from the penalty spot, stole the ball on half-way and surged forward to set-up the Iceland international.
It was just rewards for Copenhagen after they had dominated for long spells only to see Daniel Chukwa level for the Norwegian champions just after the hour.
Copenhagen will now head into the final round of the group games a point behind Stuttgart, who thumped Group E leaders Steaua Bucharest 5-1 on Thursday night.
The Danish side will be hopeful Steaua are equally as accommodating when they host them on the final day, with a wide-margin victory set to send them through.
The visitors were quickest out of the blocks with the impressive Santin's early speculative 25-yarder sailing wide before Andreas Cornelius was denied by a brilliant Espen Pettersen save.
The Molde goalkeeper was at full stretch to tip away Cornelius' header from close range.
The Danish side were rewarded for their early pressure from the penalty spot on 21 minutes after Chukwa fouled Cornelius following a corner.
Santin nervelessly stepped up and chipped the spot kick down the middle to beat Pettersen who had already dived for the corner.
Molde's hopes of progression were now in jeopardy and they almost pulled the goal back on the half-hour when Kim Christensen fumbled Jo Inge Berget's well-hit drive before gathering.
Copenhagen remained 1-0 ahead going into the break though with Santin heading a Pierre Bengtsson's cross wide.
Bengtsson thought he had doubled his side's lead eight minutes after the re-start only for Pettersen to pull of his second memorable save of the match. This time the Molde goalkeeper showed quick reflexes to tip Bengtsson's 12-yard shot wide.
Pettersen's heroics looked set to be repaid in full when Chima got on the end of Magnus Eikrem's swinging free-kick on 62 minutes to head the hosts level.
But Copenhagen rallied again and Santin stole the ball before delivering the killer pass for Gislason to net the decisive goal.