Timlin’s late intervention ensured the Shrimpers will jump above Bury and move level on points with third-placed Wycombe if they win at the JD Stadium on Tuesday night.
Exeter shaded the first half, but it was a 45-minute period where neither goalkeeper was tested.
Liam Sercombe was twice off target with efforts for the hosts, while the recalled Jimmy Keohane also spurned a good chance after good work by Ryan Harley and Clinton Morrison.
Southend’s best chance fell to Joe Pigott, but he failed to make decent contact and the ball trickled harmlessly wide of Christy Pym’s far post, while Adam Barrett was off target with a header from a corner.
Substitute Tom Nichols forced the first save of the day in the 65th minute after being set up by Keohane, but David Bentley was equal to it, while Pym made a superb fingertip save to keep out an effort from Myles Weston.
But two minutes into stoppage time, Timlin struck the decisive blow when he nipped in at the back post to poke high into the net to extend Southend’s winning run to six matches.