The visitors had dominated the opening period, with Rickie Lambert's shot brilliantly blocked by Rob Edwards.
Saints took the lead when Richard Duffy failed to deal with a free-kick at the back post and Adam Lallana took full advantage to fire into the far corner.
The Grecians equalised with their first effort at goal as Matt Taylor headed in a corner, while substitute Bertie Cozic hit a post in stoppage time.