The visitors were guilty of over-committing as Fleetwood opened the scoring against the run of play.
A quick break saw Fleetwood go two-on-two with the Shrimpers and Scotland Under-21 international McManus marked his debut with a 25-yard piledriver.
The goal opened up the game and Fleetwood could have had a second moments after the break.
Jamille Matt’s header was saved low by Southend goalkeeper Dan Bentley and McManus rattled the woodwork from Danny Andrew’s centre after Southend made a hash of clearing their lines.
Southend were still in it, Hurst forcing a low save from Fleetwood goalkeeper Chris Maxwell as the hosts again buckled under pressure.
The visitors almost found a way back when Maxwell lost the ball in a crowded box and substitute Jamie Proctor was well placed to clear off Fleetwood’s goalline.
The equaliser, when it came, was more luck than invention as Southend substitute David Worrall swung over a cross from the left, which evaded everyone in the box and nestled into the far corner.
Earlier, Fleetwood had a let-off when Cian Bolger and Myles Weston led a sweeping move to open the hosts up down the middle – Kevan Hurst relieved to see the offside flag raised as his finish was somehow dragged wide.
The Shrimpers had the momentum of promotion with them, troubling Fleetwood with a high-energy pressing game and Anthony Wordsworth was also inches away from opening the scoring from a drilled back-post cross.