Back-to-back league defeats means the Black Cats finished fifth in the overall standings.
They had been desperately poor for the opening hour of the game but some bold substitutions from Jack Ross got them level and put them in the driving seat.
Another soft goal allowed Southend to retain their League One status, however, with Sunderland now entering the play-offs with just one win in seven league games.
An indifferent run of form had left Sunderland in need of three points and a morale-boosting win.
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Ross' selection was attacking, Will Grigg and Charlie Wyke up front with Chris Maguire drifting infield from the left.
They had most of the ball early on but it was Southend United, fighting for their League One future, who created the better openings on the break.
The Black Cats failed to deal with a long ball early on and Dru Yearwood was able to break free, the midfielder denied by a fine Jon McLaughlin block.
Yearwood should have made amends moment later as Sunderland gifted possession away, the away side breaking to the byline and pulling the ball back of the edge of the box where the 19-year-old couldn't connect.
The away side were mostly limited to possession at the back but nearly went ahead when Lynden Gooch drove infield and picked out Chris Maguire with an excellent through ball. Maguire took his marker out the game with a clever first touch but fired wide on his weaker foot.
Gooch had a golden opening as Max Power drove a fine counter, but the youngster fired his cross clear of the back post.
The Black Cats seemed to be in the ascendancy, the home support panicked as their fate hung in the balance.
That tension gave way to delight just moments before the break, a corner headed back into a dangerous area where John White, with his back to goal, was able to volley into the top corner.
Bouyed by that strike Southend started the second half much the better team. just unable to convert that superiority into clear chances.
Ross mixed things up early, with Kazaiah Sterling and Luke O'Nien introduced. O'Nien dropped in behind a very attacking trio of Maguire, Wyke and Sterling, the Black Cats immediately starting to get into better area and build some overdue pressure.
They believed they should have had a penalty when Tom Flanagan released Adam Matthews, Wyke seeming certain to convert the cross before being bundled over. The referee waved play on.
It was all the away side now and they were inches away from an equaliser when Grant Leadbitter drove a long-range effort just wide.
The pressure told when a loose ball dropped for Wyke, pushed by White as he raced towards goal. Maguire stepped up and converted, though Mark Oxley did get a hand to it as he dove to his left.
Those substitutions were making a difference and almost brought about second when O'Nien flashed an excellent cross into the box, Sterling shooting first time and firing just wide.
A home winner looked unlikely but more soft defending let them into the game.
Sunderland were unable to deal with a cross into the box, substitute Stephen Humphrys with an easy finish.
Southend saw out the remaining added time with ease on another disappointing afternoon for the Black Cats.
Sunderland XI: McLaughlin; Matthews, Ozturk, Flanagan, Hume; Gooch (O'Nien, 55), Power (McGeouch, 68), Leadbitter, Maguire; Grigg (Sterling, 56), Wyke
Subs: Ruiter, Oviedo, Dunne, Connelly
Southend United XI: Oxley; Moore (Humphrys, 77), White, Turner; Bwomono, Mantom, Kienan, Hart, (Kightly, 69) Yearwood (Dieng, 71); Cox, McLaughlin
Subs: Bishop, Dieng, Lennon, Hendrie, Hutchinson
Bookings: Wyke, 39 Kiernan, 40 Humphrys, 87
Attendance: 10,779 (3.405 away)