Saints bossed the opening exchanges and shortly after Lee Barnard had smacked a venomous cross-shot against the upright, Ricky Lambert drilled a deflected 25-yard free kick past a flat-footed Jamie Jones to give them a 12th-minute lead.
The lead lasted only three minutes - Orient equalising with a Terrell Forbes header from a Charlie Daniels corner in a rare forage forward by the East Londoners.
Southampton continued to call the tune - Jones tipping over a Lambert header - but ran out of ideas.
The second half was almost a carbon copy - Barnard testing Jones and then sending a header against the underside of the Orient bar.
Grit and determination earned Orient a deserved point with Southampton frustrations culminating with a wayward Jason Puncheon shot which flew so high it struck the roof of the stand.