Two second half goals from Tranmere striker Cole Stockton saw 10 man Morecambe slip to their first defeat of the campaign.
The Shrimps lead 1-0 at the break thanks to a goal from Mark Hughes but the Morecambe skipper was then sent off in the second half and despite the best efforts of the Morecambe defence they could not hang on until the final whistle.
Tranmere enjoyed the greater share of the first half possession but it was Morecambe who looked the more dangerous going forward.
New loan signing Joe Widdowson was denied a penalty on 29 minutes when he was brought down by in the box but the visitors soon hit back and took the lead in the 38th minute with Hughes scoring his first of the season.
Jamie Devitt swung over a corner from the right, Alan Goodall headed back across goal and Hughes was unmarked in the danger area to divert the ball past a stranded Owain Fon Williams from six yards out.
The second half was a much livelier affair as Tranmere stepped up the pace and they were rewarded with a leveller just before the hour when Stockton took advantage of Shaun Beeley’s slip to run on goal and beat Barry Roche.
The goal gave Tranmere a renewed spark and when Hughes saw red on 65 minutes for an off-the-ball incident with Kayodi Odejayi the Shrimps were forced to defend for the rest of the game.
It was Stockton who broke Morecambe’s hearts and earned the points for Rovers with a 90th minute strike.
Matt Hill chipped the ball into the Morecambe area and Stockton reacted quicker than the Morecambe defence to divert the ball past Roche.
Tranmere Rovers: Fon Williams, Holmes, Ihiekwe, Donacien, Hill, Rowe, Laird, Power, Baggie, Richards (rep Odejayi 57), Stockton. Subs not used: Holness, Kirby, Woodards, Ramsbottom, Bruna, Gill.
Booked: Power, Baggie, Odejayi.
Morecambe: Roche, Beeley, Parrish, Hughes, Widdowson, Goodall, Wright, Fleming (rep Redshaw 78), Devitt (rep Doyle 68), Mullin (rep Amond 68), Ellison. Subs not used: Arestidou, Kenyon, Sampson, Williams.
Sent off: Hughes
Referee: Mark Haywood