Walcott, who has been left on the bench amid his refusal to extend a contract that expires next summer, poached the opening goal, before striker Olivier Giroud headed the visitors into a surprise two-gaol lead.
But Holland forward Klaas-Jan Huntelaar caused Arsenal jitters by scoring just before half-time and Schalke deservedly equalised through Jefferson Farfan to maintain top spot in Group B.
“I just want to play,” said Walcott. “Hopefully now I can get a run in the team because I feel I fully deserve it. It was a good point in the end. It would have been a fantastic victory but Schalke are a tough side.”
Wenger, whose side lie second but look very well placed to qualify, praised Walcott, who shrugged off illness to play last night.
“He did well,” he said. “He had a positive attitude and was fresh as well. He was the only one you always felt could make a difference and it was no coincidence he had the chance in the final minute.”
Wenger axed under-fire Andre Santos and Aaron Ramsey for Laurent Koscielny and Walcott, the club’s top scorer with eight despite only four starts. Yet it was against the run of play when, in the 18th minute, Walcott gobbled up a loose ball following a last-ditch tackle on Giroud to round Lars Unnerstall.
Eight minutes later Giroud flung himself at Lukas Podolski’s whipped left-wing cross and headed the Gunners’ second goal.
The home side hit back just moments before the interval, when Huntelaar drilled left-footed first time across Mannone. With gnawing inevitability Schalke levelled in the 67th minute, when Afellay’s cross reached Farfan and he lashed in via Arsenal captain Thomas Vermaelen.