Madrid defended well and for all Liverpool's possession there were long periods they lacked the necessary guile to break down a well organised Spanish rearguard.
Liverpool needed only three more goals to reach 300 in European competition and almost got the first of these after only 70 seconds.
Daniel Agger totally mishit following a corner and that was followed by half hearted appeals for a penalty as the ball hit a Madrid defender,
That was about as exciting as it got in the first half as Liverpool struggled to break down an obdurate Atletico defence.
Xabi Alonso did release Robbie Keane whose 20 yard shot flashed narrowly wide.
The Irishman probably had the best chance when through one on one with the keeper but Leo Franco anticipated well and gathered the ball.
Madrid finally broke out of their defensive shell and Simao failed to connect from six yards.
Then on 37 minutes Atletico took a shock lead and gave their noisy fans something to cheer about.
A quick break ended with Antonio Lopez firing in a cross which Maxi Rodriguez took in his stride, brushed past Jamie Carragher to angle a shot past Pepe Reina.
Liverpool began the second half with much more urgency and again appealed in vain as Luis Perea appeared to handle in the area,
Agger then headed narrowly over from a free kick as The Reds poured forward at every opportunity.
The Danish defender then failed to connect cleanly as the ball broke to him and Franco easily saved.
Atletico were struggling to get out their own half but a couple of quick breaks did show Liverpool had to be watchful of over committing to attack.
But Liverpool have made a habit this season of saving games late and in the forth minute of injury time Pernia and Gerrard clashed going for a header and the linesman adjudged the Madrid player to have impeded the Reds skipper.
Gerrard coolly converted from twelve yards amidst uproar from the Madrid players.
"There had been possible penalties before, a hand ball, but if this was a foul outside the penalty area it would have been a free kick so it was a penalty.
"We had three or four chances to score in the second half so we had to wait until the end to score.
"It was important for us not to lose and it shows the character of the side who five or six times this season have come from behind. We kept attacking and attacking and kept going until the end.
"You have to do that if you want results.
"We now have one more point than before, if it was important to win it was even more important not to lose."