Chris Eagles, Steven Thompson and substitute Kevin McDonald were on target as the Clarets came from behind to avoid a Carling Cup upset and maintain their unbeaten start to the season in a cracking cup tie at the new Globe Arena.
Morecambe threatened a repeat of their first-round shock of Coventry City when they took an early lead through Phil Jevons.
But the League Two outfit was finally overcome by a Burnley side which underlined its squad strength as boss Brian Laws made nine changes from the team which had started last Saturday's 3-0 win over Leicester City.
Eagles and Thompson were among those in from the start as only the influential Wade Elliott and Clarke Carlisle, captain on the night, were pressed back into duty.
And the pair both seized their chance to impress in leading the Clarets' fightback as Laws' men booked their place in the third round.
Thompson laid on a stunning equaliser for Eagles before the break and then struck on the hour when he converted a penalty won by Eagles on the day he agreed a new two-year deal at Turf Moor.
Thompson scores from the spot
McDonald had been forced to settle for a place on the bench but still had time to make an impact as his 83rd-minute thunderbolt completed the fightback and secured the Clarets' place in Saturday's draw for the last 32 and raised hopes of another cup run.
The Clarets' much-changed side took time to settle and Morecambe quickly punished their nervy start.
The underdogs looked anything like a side without a win in the basement division as they moved the ball around swiftly and they took the lead with a goal that wouldn't have looked out of place on a higher stage.
The impressive Chris Shuker sparked the danger ball with a into Jevons which the former Everton youngster laid off to Mark Duffy.
Duffy was faced with a two white shirts but managed to squeeze a pass back to Jevons who had got behind the Burnley defence to hook a shot past Lee Grant and into the bottom corner.
Morecambe score as the Clarets appeal for offside
Burnley responded with Jay Rodriguez glancing a header wide from Wade Elliott's fine cross and Eagles putting a snap-shot into the midriff of goalkeeper Barry Roach.
But Morecambe remained undaunted and with 22 minutes gone were a whisker away from doubling their lead.
Shuker was again involved as he met a cross from Paul Scott to tee up Jevons and his close-range shot on the turn looked to be heading in until Grant made a vital block to deflect the ball past the post.
The Clarets needed something to take the sting out of the Shrimps and gain a foothold in the game and it came after half an hour with a cracking leveller.
The hard-working Jack Cork provided the ammunition with a ball into the Morecambe penalty area and Thompson's cushioned lay-off was perfect for Eagles run onto and crash a right-footed shot past Roach from 16 yards.
Eagles takes the plaudits after levelling
Eagles' first goal of the season didn't turn the tide completely but Burnley suddenly attacked their greater menace and had two chances from to go in front from set-pieces just before the break.
Eagles delivered on each occasion with Leon Cort nodding down a free-kick for Clarke Carlisle to volley over and Rodriguez then heading a corner wide after he and Edgar had opened up the Morecambe defence.
The 5,003 inside the Globe Arena represented a record crowd for Morecambe's new stadium and the home fans were nearly celebrating again ten minutes into the second half.
Burnley had dominated the opening exchanges as they looked to get the job done but when the Shrimps were awarded a free-kick for a foul by Elliott just outside the penalty area, Laurie Wilson smacked a free-kick against the bar.
That underlined the tightness of the tie but five minutes later the Clarets took a grip as they went 2-1 up from the penalty spot.
Again Eagles was key as he ran onto a fine pass from Brian Easton and after going past Darren Moss was brought down by the Morecambe full-back.
With no Graham Alexander to take the responsibility Thompson grabbed the ball and coolly rolled in his first penalty for the club.
With Eckersley going into the book for handball and then earning another lecture from referee Graham Salisbury moments later, Laws took no chances in withdrawing the full-back and sending on McDonald as Burnley looked to maintain the initiative.
And immediately McDonald had a chance on the break but his scuffed cross failed to find a team-mate after Rodriguez had launched a counter-attack.
A third goal would have been welcome for the Clarets to finally kill off their spirited opponents and after Eagles had forced Roach into a flying save the winger had a chance to bag the third but couldn't provide the finish from another Rodriguez break-away.
Any late nerves were soon soothed, though, as McDonald secured the Clarets' passage through as he lashed a 25-yard drive, with the aid of a slight deflection, into the roof of the net.
Celebrations with McDonald
That was the key for Chris Iweulmo to sit back back down on the bench and Laws instead gave senior debuts to Michael King and Wes Fletcher for the final few minutes of an ultimately successful night.
Burnley: Grant, Eckersley (McDonald 67), Cort, Carlisle, Easton, Edgar, Cork, Eagles (King 86), Rodriguez (Fletcher 90), Thompson, Elliott. Subs: Iwelumo, Paterson, Wallace, Jensen.
Morecambe: Roach, Moss (Mullin 72), McCready, Parrish, Wilson, Scott, Stanley (Drummond 81), Fleming (Hunter 80), Duffy, Jevons, Shuker. Subs: Bentley, Haining, Walker, Spencer.
Booked: Burnley: Eckersley 62, Rodriguez 66
Morecambe: Scott 37, Stanley 76, Duffy 78