The home side could not break down a solid Shrimpers defence and the visitors won it when Tomlin went clear with seven minutes to play.
Chesterfield shaded the possession in a low key first half but neither goal came under threat until Marc Richards thundered a 25-yard free-kick against the underside of the crossbar in the 41st minute before forcing goalkeeper Paul Smith to push out another fierce strike 60 seconds later.
Southend continued to frustrate the Spireites after the break, although Danny Whitaker saw a dipping 20-yard shot just clear the bar before a low cross almost fell to Jack Lester.
The visitors had created little since the opening minutes but they stunned the hosts with a sucker punch in the 83rd minute.
Michael Timlin robbed Sam Togwell inside the Chesterfield half and sent Tomlin clear and he placed a right-foot shot inside Tommy Lee's left-hand post.
