The England international made his first appearance at St Mary's since leaving in 2006 but he, and fellow former Saint Alex Oxlade-Chamberlain, had to make do with a point.
Southampton, now out of the relegation zone, took a deserved lead in the first half through Gaston Ramirez and matched their visitors for most of the contest.
But Arsene Wenger's frustrated Arsenal, who dropped points in the race for the UEFA Champions League, levelled before half-time when Brazilian forward Guly turned Walcott's free-kick into his own goal.
Much of the build-up to Tuesday's game surrounded graduates of Southampton's fabled Academy.
Both Walcott and Oxlade-Chamberlain started at the place they once called home, while speculation was rife that Luke Shaw, the latest star off the production line, could soon follow them to Emirates Stadium.
Clear-cut opportunities were in short supply in the first half and the opening goal came in the 34th minute thanks to shambolic defending rather than any moment of genius.
Arsenal failed on a number of occasions to clear the ball and, after seeing a shot blocked, Jason Puncheon pulled back for Ramirez to fire home just inside the 18-yard box.
The lead lasted just seven minutes, though, as Puncheon gave away a free-kick wide on the left.
Walcott swung it in and Guly directed past his own goalkeeper at the near post to send the 3,141 visiting fans into raptures.
Arsenal thought they had a second before the break as Walcott found a way past Artur Boruc, only for it to be chalked off for offside.
The home side responded well when the teams re-emerged for the second half, with a Rickie Lambert header across the six yard box just evading his team-mates.
Both managers made changes in a bid to find a winner, with Mikel Arteta coming close with a fierce 25-yard strike.
Wojciech Szczesny parried a late Puncheon strike and Maya Yoshida cleared a later cross as the match ended level, propelling Saints out of the drop zone.