The Liverpool goalkeeper saw the ball rebound off him after Marouane Chamakh had hit the post in the final minute at Anfield to cancel out David Ngog's strike.
The goal was reward for a late spell of Arsenal pressure but it was unfortunate for Liverpool, who had survived most of the second half unscathed after the sending-off of Joe Cole.
The big-name summer signing from Chelsea was dismissed on his league debut for a reckless challenge on Arsenal debutant Laurent Koscielny.
Koscielny himself also received a red card, but not until moments before the final whistle when he earned a second caution for handball.
The equaliser denied Liverpool what would have been only their fourth victory over the Gunners in their last 19 league meetings.
It remains to be seen how much the new wave of optimism which has swept into the club since Roy Hodgson was appointed as manager has been punctured.
One of the reasons for the upbeat mood had been Cole's arrival but while the midfielder's first league start was one to forget, Hodgson did coax a solid showing from wantaway Javier Mascherano.
Fernando Torres was left in reserve, and later entered to a huge ovation after pledging his future to the club and recovering from a groin injury, but Arsenal missed two of their bigger stars more.
Cesc Fabregas and Robin van Persie were both said to be lacking match-fitness and while the former was absent altogether, the Dutchman made only a late appearance.
Thomas Vermaelen tested Reina early on with a fierce free-kick but aside from that, the first half was almost devoid of action until exploding into life in the closing moments.
First Glen Johnson had a shot tipped over by Manuel Almunia and Ngog then had a header cleared off the line from the resulting corner.
The complexion of the game then changed completely in stoppage time as Cole was sent off for his lunge at Koscielny.
Koscielny returned to the dressing room on a stretcher at the interval but ran out to start the second period as normal.
He was greeted by boos from Liverpool fans but replays of the tackle suggested that, although the initial decision may have seemed harsh, the law had been applied correctly.
Liverpool seemed determined not to let their numerical disadvantage bother them and made a blistering start to the second half.
They claimed the lead within two minutes of the restart as Mascherano threaded a ball into the box for Ngog and the Frenchman finished unerringly at the near post.
It was his fourth goal of the season after three in Liverpool's first Europa League qualifying tie.
Not content with that, the Reds pushed forward again and Martin Skrtel headed wide from a dangerous free-kick taken by Steven Gerrard.
Ngog had an even better chance when he leapt to reach another Gerrard set-piece but could not direct his header on target.
Dirk Kuyt created another fine chance after good work on the right but no one could turn in his ball across goal.
Liverpool were reduced to nine men when Daniel Agger left the field for treatment after all three substitutes had been used.
Arsenal stepped up the tempo and Tomas Rosicky showed great control with a slaloming run into the area before seeing his shot touched over by Reina.
Maxi Rodriguez then cleared after a desperate goalmouth scramble.
The pressure eventually told in the last minute as Reina failed to grasp the ball after Chamakh hit the post from Rosicky's cross.
Gerrard almost snatched victory as the game went into five minutes of stoppage time but Almunia kept out his free-kick.
The game ended on more controversy as Koscielny was dismissed for a second cautionable offence.
Liverpool: Reina, Johnson, Carragher, Agger, Skrtel, Gerrard, Jovanovic (Maxi 65), Mascherano (Lucas 78), Kuyt, Cole, Ngog (Torres 74). Unused substitutes: Cavalieri, Aurelio, Babel, Kelly.
Arsenal: Almunia, Sagna, Vermaelen, Koscielny, Clichy, Eboue (Walcott 59), Nasri, Diaby (van Persie 76), Wilshere (Rosicky 60), Arshavin, Chamakh. Unused substitutes: Fabianski, Vela, Song, Gibbs.
Referee: M Atkinson (W Yorkshire).
Hero: James Milner
Anyone who knew him at Leeds United will not have been surprised by the manner in which he not only turned out for Aston Villa amid negotiations for a move to Manchester City but also put in a superb performance which included scoring.
Villains: Champions Chelsea
Blackpool's stunning 4-0 win over Wigan had seen them top the first Premier League table but the glory was temporary as Chelsea kicked off in the evening match and spanked six goals past West Bromwich.
Blackpool, who defied all the gloomy predictions pre-match to get an immediate win under their belts.
Wigan, naturally, who have immediately been bracketed among those expected to fall out of the division come May.
Liverpool managing director Christian Purslow admits his club need to find new owners "as soon as possible" but will not make any hasty compromises on their future.
Purslow insists unearthing the right buyer is much more important than establishing the quickest one.