The Gunners looked to be on course for victory in Germany as first-half goals from Theo Walcott and Olivier Giroud put them in control.
But a Klaas-Jan Huntelaar strike just before half-time gave Schalke hope and they piled on the pressure after the break and were rewarded for their endeavours on 67 minutes by Jefferson Farfan's equaliser.
It had all looked bright for Arsenal midway through the first period. They took the lead when a mistake by Roman Neustadter allowed Giroud through on goal and although skipper Benedikt Howedes got back to take the ball off the Frenchman's foot, Walcott was on hand to pounce on the loose ball.
Giroud doubled the lead on 26 minutes after his persistence saw him feed Lukas Podolski and the French international took advantage of slack marking by the Germans to power a header home.
Arsene Wenger's half-time team talk was made more difficult in stoppage time when Huntelaar fired home with his left foot after a slip by Santi Cazorla allowed Lewis Holtby to feed the Dutchman to hammer beyond Vito Mannone.
Giroud missed a great chance to extend the visitors' lead within three minutes of the restart but he made a hash of his volley after more great work down the left by Podolski.
He could have been made to pay for his miss but Huntelaar failed to beat Mannone when one on one with the Arsenal keeper. The Italian also did well to parry a deflected effort from Jermaine Jones as Schalke pushed for the equaliser.
The Germans had a huge shout for a penalty on 54 minutes when a goalbound shot from Howedes struck Per Mertesacker on the arm but referee Nicola Rizzoli waved away their appeals.
However, the hosts were on level terms when Thomas Vermaelen could only deflect Farfan's far post effort into his own net.
The final quarter of the game was very much backs to the wall for the visitors but they held out to claim a welcome point with the Gunners' trip to Greece to face Olympiakos - winners over Montpellier - likely to prove pivotal.
They even had chance to snatch victory at the death but Walcott was denied by the legs of keeper Lars Unnerstall.