The unmarked Simao drilled home a low shot with seven minutes remaining to cancel out Robbie Keane's early opener for Liverpool as the two sides, having each won their first two games, remained unbeaten in Group D.
Liverpool controlled the first half and held a deserved lead at the break but Atletico, who had been unbeaten in their previous six home meetings with English opposition, fought back to salvage a point which could ease the pressure on under-fire coach Javier Aguirre.
The Champions League anthem at the start of the match was greeted by jeers and whistles from the home fans, while the Atletico supporters behind the goal also turned their backs to the pitch in protest against the punishment handed out by UEFA last week.
Atletico were given a three-match stadium ban in Europe and fined by UEFA following crowd disturbances and accusations of racism during their Champions League home match against Marseille.
Atletico have appealed against the punishment, which is why Wednesday's match was able to go ahead at the Vicente Calderon and not at least 300 kilometres away from Madrid.
However, there was no obvious repeat of those crowd disturbances or racist chanting during Wednesday's clash, which saw Liverpool quickly settle into their stride.
Benitez's troops, unbeaten in their last 15 matches, could barely have asked for an easier opening 45 minutes as they took an early lead through Keane before comfortably containing a toothless Atletico.
Keane's goal came not long after young Atletico midfielder Ignacio Camacho had headed over the first chance of the match following a Simao free-kick.
Liverpool captain Steven Gerrard created the chance with a superb pass through for Keane, who beat the Atletico offside trap before coolly slotting low past Leo Franco.
That was just the start Liverpool would have been hoping for and Gerrard and Xabi Alonso both then tried their luck from distance before Keane spurned a decent opening to double Liverpool's lead.
He again escaped the attentions of his markers to get on the end of Gerrard's right-wing cross, but the Irishman attempted an ambitious flick and ended up missing the ball.
At the other end a much-changed Atletico, who had lost their previous three league matches against Sevilla, Barcelona and arch rivals Real Madrid, looked devoid of ideas going forward in the first half.
The hosts finally gave their fans something to get excited about in the 40th minute when former Manchester United striker Diego Forlan unleashed a 25-yard drive that flew just wide of Jose Reina's far post.
Aside from that effort though, the Liverpool custodian, one of four Spanish players in the Liverpool line-up, had precious little to do before the break.
Atletico coach Aguirre, under pressure following three successive league defeats, decided it was time to change things around at the break and he sent on star striker Sergio Aguero for former Liverpool player Luis Garcia.
That change immediately appeared to give Atletico a lift as they twice came close to an equaliser soon after the break.
The first opening saw Maniche pick up a pass from Forlan on the far side of the area before firing in a shot that flew into the far corner of the net.
However, the Portuguese was left with his head in his hands - along with the majority of the stadium - as he noticed the offside flag had gone up.
From an almost identical position moments later Simao then drilled in a shot which Reina brilliantly helped onto the post and then gathered at the second attempt as Liverpool rode their luck.
Reina could do little about the goal that brought Atletico back on level terms in the 83rd minute however.
Simao was left in acres of space on the far side of the area and, after Forlan had picked him out, he drilled a low left-footed shot past the diving Reina to level the scores up at 1-1.
That goal set the stadium rocking and gave Atletico a huge boost, and Miguel then tested Reina with a well-struck volley soon afterwards.
Liverpool could have silenced the home crowd in the 89th minute though when substitute Ryan Babel sent a diving header just wide of the Atletico goal from close range, but the match would end up finishing all-square.