Arsene Wenger's side rarely threatened on the south coast in a game that the relegation-threatened hosts looked more likely to win.
Saints proved a much different proposition to the team that Arsenal ruthlessly dispatched of 6-1 in September, taking the lead after 34 minutes.
It was a goal that the Gunners should have prevented but, after wasting several chances to clear their lines, Gaston Ramirez fired the hosts in front.
The lead lasted seven minutes, though, as Theo Walcott, making his first appearance at St Mary's since leaving in 2006, whipped in a free-kick that Do Prado could only prod into his own goal.
It proved the evening's decisive moment as, try as they might, Southampton were unable to find a winner in a second half they dominated.
Much of the build-up to today's game surrounded graduates of Saints' fabled academy.
Both Walcott and Alex 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 the Emirates Stadium.
Arsenal began strongly at St Mary's and Santi Cazorla saw a long-range strike deflect just wide in the fifth minute.
Southampton's Artur Boruc, making his first appearance since October 28, was fortunate that his fumble at the resulting corner did not cost his side.
The Polish goalkeeper was looking more than a little rusty in terms of catching and kicking, although Saints were beginning to show signs of life.
The striker was offside anyway and Arsenal soon returned to the attack, with Yoshida having to react smartly to block a Lukas Podolski strike.
The Japan international again had to be on his toes to stop Walcott getting a shot on goal after a break in play for Jack Wilshere to receive treatment.
Neither side were creating much in the final third and the opening goal came 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 in the 34th minute.
The lead lasted just seven minutes, though, as Puncheon gave away a free-kick wide on the left.
Walcott swung it in and Do Prado 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 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 Lambert header across the six yard box just evading his team-mates.
Arsenal goalkeeper Wojciech Szczesny proved his worth in the 56th minute by denying the hosts twice in quick succession.
The 22-year-old palmed a threatening Do Prado effort behind and from the resulting corner he had to react quickly to stop Lambert bundling home.
Wenger brought on Olivier Giroud for the ineffective Podolski in a bid to change the game, although Saints again wasted a chance when Lambert slipped in the box with the goal at his mercy.
Morgan Schneiderlin provided the cross and was then booked for a foul on Cazorla, before Puncheon fired into the side-netting from an acute angle and Ramirez struck over.
Walcott stung the palms of Boruc on a rare Arsenal move forward, before Ramirez saw a goal ruled out for a foul.
Both managers made changes in a bid to find a winner, with Mikel Arteta coming close with a fierce 25-yard strike.
Gervinho hit the side-netting as Arsenal again came close, before another substitute, Steve de Ridder, was booked for a foul on Sagna.
Szczesny parried a late Puncheon strike and Yoshida cleared a later cross as the match ended level, propelling Saints out of the drop zone.