Few would have predicted an outcome in Rovers' favour at half time, following an opening period spent almost entirely on the back foot.
But goals from John Marquis, Mallik Wilks and Tommy Rowe saw Rovers surge into a three goal lead by the 70th minute.
The drama was not over as Tom Hopper put a small element of doubt on the result with 15 minutes to go before ex-Rovers striker Theo Robinson reduced the deficit to one with only four minutes remaining.
But, despite constant Southend pressure through eight minutes of added time, Rovers held on for the win.
There were few surprises in McCann's first starting XI following a pre-season of building.
Tough decisions at goalkeeper and centre half were settled with the selection of Marko Marosi and Joe Wright while Ali Crawford and Mallik Wilks were handed their debuts.
The depth in the squad was reflected by those not involved, including Alfie Beestin and Luke McCullough who were dealt the harsh blow that many will likely face over the course of the campaign.
Those selected found themselves under pressure throughout a first half spent firmly on the back foot.
Rovers simply could not get out of their own half as Southend pushed forward.
It resulted in plenty of nervy moments which only seemed to increase the panic among the Rovers defence.
Clearances were rushed and the ball simply would not stick with a front line that became increasingly isolated as the midfield was pushed deeper and deeper.
How Southend failed to score during a period of overwhelming dominance will be a point of consternation for those at Roots Hall for some time.
A big reason for that was Marosi, who turned in an inspired performance in goal for Rovers.
Marosi held an early header from Hopper before pushing away a curling effort from the lively Michael Kightly.
He then denied an excellent free kick from Ben Coker at the foot of his post before reacting superbly after a Simon Cox shot looped up off Andy Butler's leg.
Kightly clipped the post after being put through one-on-one with Danny Andrew hacking away a clearance on the line.
It took Rovers 43 minutes to muster a genuine effort on goal when Crawford curled wide from the edge of the box.
McCann will certainly have been the happier manager at the break after his side survived the onslaught.
And they looked much more of a composed outfit at the start of the second half as they took care of the ball much better.
But it was still somewhat against the run of play when Marquis fired them in front on 51 minutes.
Latching onto a superb lofted ball from Rowe, he cut back onto his right foot and curled into the far corner from the angle.
Wright delivered a superb goal saving block just seconds later.
And it was made to count on 58 minutes when Wilks netted on his debut with a real goal from nothing.
Receiving the ball on the edge of the box with his back to goal, the Leeds United loanee turned and shot in one swift motion, drilling the ball in at the near post.
Wilks was revitalised and powered a shot on goal which drew a fine save from Mark Oxley.
By 70 minutes, Rovers looked to be out of sight.
Rowe received a short corner from Crawford and cut into the box before shooting with his right foot. The effort was tame but missed by two defenders before rolling into the far bottom corner.
Just when it appeared the game was over, Southend put the result in some doubt when Hopper turned the ball over the line in from close range after a goalmouth scramble.
Southend piled on the pressure and reduced the deficit to on when Robinson smashed in from close range after a lay-off from Hopper
And the hosts threw the kitchen sink at Rovers, particularly as the game moved into eight minutes of time added on.
But Rovers held on to secure a breathless opening day triumph.
Southend: (4-4-2) Oxley, Demetriou, Turner, Lennon, Coker, McLaughlin (Barratt 65), Mantom, Hyam, Kightly (Dieng 74), Hopper, (Robinson 65). Subs not used: Bishop, Bwomono, Klass, White.
Rovers: (4-3-3) Marosi; Mason, Wright, Butler, Andrew (Amos 66); Crawford (Blair 76), Whiteman, Rowe; Coppinger (Kiwomya 59), Marquis, Wilks. Subs not used: Lawlor, Anderson, Kane, May.
Referee: Craig Hicks (Surrey)
Attendance: 7,147 (591 away)