Flo struck just five minutes after being thrown into the action before Rui Marques saw his header glance in off the bar and Jermaine Beckford coolly dispatched a volley in stoppage time.
Alan Thompson had given Leeds the perfect start during his first appearance at Elland Road as the club's new captain.
He took only two minutes to curl an unstoppable free-kick past Southend keeper Darryl Flahavan after lively striker Beckford was hauled down by Peter Clarke.
It was a moment that sent the home support into raptures as Leeds continue to try to overcome their 15-point penalty and left Southend temporarily stunned.
But Steve Tilson's side regrouped and gradually began to look the more threatening of the two sides.
Alan McCormack robbed Thompson in the Leeds half before thundering a left-footed shot on to the far post as Casper Ankergren made a desperate dive to his right.
Then Matt Harrold failed to take advantage of three chances in four minutes as the visitors continued to press.
He just missed Jamal Campbell-Ryce's cross, then forced a reflex save from Ankergren sixty seconds later before watching his third attempt - a 20 yard effort - deflect just wide of the post after Frazer Richardson made an important block.
Beckford's pace was proving Leeds' most potent threat and the young striker should have doubled the hosts advantage, only to embarrassingly smash a close range volley well wide.
Flahavan also denied a good header from Jonathon Douglas, but Leeds were hit with a blow when Ian Westlake was forced off just before the break after suffering an ankle injury.
Adam Barrett eventually equalised for the Shrimpers with a 70th minute header, but Flo stole the show as Leeds grabbed their third win in eight days.