It is a headache for boss Rafael Benitez ahead of Sunday's game at Chelsea, with Fernando Torres already struggling with a hamstring problem.
Benitez surprisingly left in-form Dirk Kuyt on the bench and played Keane as a lone striker - but it was a decision that reaped rewards with a priceless early strike.
Steven Gerrard was the creator with a trademark through ball, which the Republic of Ireland striker took in his stride before calmly sliding a finish beyond Atletico keeper Leo Franco.
Replays suggested Keane was offside - and it was not to be the only contentious decision of the game.
Liverpool exercised almost total domination in the early exchanges, with Xabi Alonso shooting over and Keane wasting a glorious chance after 22 minutes when he tried to over-elaborate in front of goal from Gerrard's cross and failed to make any contact.
Diego Forlan finally fashioned a chance for Atletico five minutes before the interval with a shot on the turn that flashed just wide with Reina beaten.
Liverpool suffered a blow seven minutes after the break when Keane limped off to be replaced by Kuyt. It also co-incided with Atletico's best spell following the half-time introduction of the exciting Sergio Aguero.
Atletico were desperately unlucky not to equalise after 55 minutes when Maniche's fine finish was ruled out by a linesman's flag, even though he was clearly onside, although Benayoun appeared to suffer a similar injustice moments earlier.
Liverpool were then thankful to keeper Reina when his fingertips diverted Simao's shot on to an upright.
The visitors were starting to look jaded, and Benitez replaced captain Gerrard with the pace of Ryan Babel on the hour.
But just as it looked like they had weathered the storm, Atletico drew level with seven minutes left.
Jamie Carragher misjudged a long ball to let Forlan in, and he found Simao, who drove a top-class finish across Reina into the bottom corner.
Atletico were scenting victory, and Reina had to be alert to turn a drive from Miguel over the top.
But Babel wasted a glorious opportunity to snatch the win for Liverpool after 88 minutes, when he somehow headed Kuyt's cross wide with the goal at his mercy.
It was the final chance of the game - with the draw leaving both clubs still in a perfect position to qualify for the knockout phase.
Liverpool manager Rafael Benitez
"You have to finish when you have the chances. We were trying to find the perfect pass. We were in their final third and all we were doing was passing it.
"We were playing well and we had control until we got to the final third. We tried to be too precise, tried to give the perfect pass and didn't finish when we should have done.
"We have one more point now and it's not a bad position to be in, but if you concede after 83 minutes then you have to be disappointed.
"I'm happy with the game we played in the first half and to start the second. I'm disappointed with the chances we had to finish the game and didn't take though."
Atletico Madrid: Franco, Seitaridis, Perea, Dominguez, Antonio Lopez, Camacho (Raul Garcia 72), Maniche, Luis Garcia (Aguero 46), Simao, Forlan, Sinama Pongolle (Miguel 75).
Subs Not Used: Bernabe, Pernia, Heitinga, Paulo Assuncao.
Goals: Simao 83.
Liverpool: Reina, Arbeloa, Carragher, Agger, Dossena, Mascherano, Alonso (Leiva Lucas 75), Benayoun, Gerrard (Babel 61), Riera, Keane (Kuyt 53).
Subs Not Used: Cavalieri, Aurelio, Pennant, Darby.
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