The Russian, introduced in the second half, produced two superb finishes as the Gunners maintained their promising build-up to the new campaign.
There was also a welcome home return for Czech winger Tomas Rosicky, who had been out of action for some 18 months with a string of niggling injuries - and his availability for the build-up to the new campaign will be welcome boost to manager Arsene Wenger following the loss of Samir Nasri to a broken leg.
Wenger had named a mixed side, which included Vito Mannone in goal and Robin van Persie, last season's leading scorer, as captain with Cesc Fabregas one of 10 substitutes.
The Gunners have seen Emmanuel Adebayor and Kolo Toure depart for Manchester City, but eventually made their dominance pay when Arshavin slipped in a late winner.
The Spanish side, who started with former Gunner Jose Antonio Reyes in attack and were captained by ex-Manchester United forward Diego Forlan, could yet face Wenger's men again in competitive action next month in the Champions League play-off.
Following a period of appreciation for former England manager Sir Bobby Robson, who died on Friday, aged 76, Madrid midfielder Tomas Ujfalusi hit the post with an early far-post header, before Arsenal asserted control.
Rosicky's previous appearance at Emirates Stadium came back on January 26 2008, against Newcastle in the FA Cup, with the complicated knee and hamstring problem first ruling him out of the European Championships then all of the last campaign.
The pacy Czech wideman, though, looked sharp and had a well-taken effort ruled out for offside after seven minutes.
Emmanuel Eboue, who has been linked with a move to Fiorentina, looked dangerous down the other flank as the hosts pressed.
Following a flowing counter-attack, when the ball was switched across field to young Wales midfielder Aaron Ramsey, van Persie fired a half-volley wide.
Atletico made a change just before the break, when Florent Sinama-Pongolle, who had spells in England with Liverpool and Blackburn, picked up an injury and was replaced by Maxi Rodriguez.
Eboue had switched flanks to the left, and forced a good reaction save from the Madrid keeper when he cut inside the penalty box.
Rosicky was given a well-earned breather, one of three players substituted at the start of the second half, replaced by youngster Fran Merida, with Gael Clichy and Jack Wilshere coming on for Armand Traore and Eboue respectively.
Arsenal started brightly as van Persie saw his clever back-heel cleared off the line by John Heitinga before Nicklas Bendtner fired over.
A slick move from 17-year-old Wilshere on the far by-line saw the ball pulled back for Ramsey, but the Wales midfielder shot straight at the keeper.
With 24 minutes to go, Arsenal made another triple substitution, with Fabregas replacing Ramsey, Eduardo coming on for Bendtner and Arshavin for van Persie.
The Gunners continued to press, with the impressive Wilshere the main outlet.
However, Rodriguez almost caught them out when he latched onto a loose ball and dashed into the right side of the Arsenal box only to drag his shot wide.
Substitute Borja Baston then tried his luck from 25 yards, with Mannone almost left red-faced as he spilled the wet ball just past the post.
The Gunners looked to have snatched a winner with just four minutes left when Fabregas lofted the ball over to the back post from the right, where Arshavin arrived to volley past Sergio Asenjo.
However, German Pacheco beat the offside trap, somewhat dubiously, to slot in an equaliser.
There was, though, just enough time for Arshavin to latch onto a poor backward header from Ujfalusi and tap the ball round the keeper before sliding it into the net from the tightest of angles.
Arsenal play Rangers on Sunday, with the Scottish champions having beaten Paris St Germain in the Emirates Cup opening game.