Mirko Vucinic also failed with his spotkick for the hosts, while Eduardo da Silva was the only player to come up short for the London club.
Brazilian defender Juan had levelled the tie on nine minutes, blasting in from close range after a Francesco Totti ball was allowed to zip across the face of goal with Rodrigo Taddei cleverly letting the ball slip through his legs.
Things started going badly for the home side before kickoff when defender Philippe Mexes was ruled out with flu after they had already lost midfielder Daniele De Rossi through suspension and several regulars through injury.
They suffered an additional blow in the 28th minute when goalscorer Juan came off hurt, forcing coach Luciano Spalletti to bring on former Arsenal forward Julio Baptista and reorganise his team.
But, after making the better start, Roma remained the more dangerous side and were unlucky not to get a penalty before halftime when Marco Motta went down after a clumsy challenge by Gael Clichy.
Both sides came out intent on attack after the break which produced action at both ends. The Londoners mismanaged some promising counter-attacks, while Baptista squandered a glorious chance to extend Roma's lead in the 79th when he got himself in a tangle with the goal gaping.
The visitors were on top at the end of regulation time when Robin van Persie came close to scoring with a deflected effort that went narrowly wide.
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