But in the 78th minute Chris Greenacre arrived at the far post to head in a deep cross from Chris Shuker for his third goal of the season.
Then deep in injury time, Shuker flicked home the second goal from fully 35 yards when he caught Albion keeper Michels Kuipers well off his line.
It was a poor finish all round for Albion as defender Andrew Whing was dismissed in the 90th minute for his second yellow card.
But Brighton boss Dean Wilkins said he had asked the referee to take another look, claiming the second yellow was a case of mistaken identity.
Both sides struggled to make an impact in the opening half.
Greenacre had the best chance for Tranmere in the 30th minute but fired inches wide from a headed by pass by Gareth Taylor.
Bas Savage brought a diving save from Rovers keeper Danny Coyne in the 25th minute.
Then Coyne was at his best in the 33rd minute when tipping over a power header by Guy Butters which followed a Dean Cox free-kick.
But in the main, Albion created little and they failed to really trouble Coyne throughout the second period.
Butters was excellent in the Albion back four and Dean Cox and Adam El-Abd tried their best in midfield.
Steve Davies was always lively for the winners and Ian Goodison and Shane Sherriff did little wrong in defence.
In the main it was a disappointing game for the fans.
It produced a number of bookings - Greenacre, Steve Jennings and Davies were the Tranmere men cautioned, while Cox of Albion also went in the book along with Whing.
Craig Curran was sent on by Rovers as a 75th minute substitute for Taylor and made an immediate impact with a part in the build-up to the crucial first goal.
Then deep in injury time, Shuker flicked home the second goal from fully 35 yards when he caught Albion keeper Michels Kuipers well off his line.
It was a poor finish all round for Albion as defender Andrew Whing was dismissed in the 90th minute for his second yellow card.
But Brighton boss Dean Wilkins said he had asked the referee to take another look, claiming the second yellow was a case of mistaken identity.
Both sides struggled to make an impact in the opening half.
Greenacre had the best chance for Tranmere in the 30th minute but fired inches wide from a headed by pass by Gareth Taylor.
Bas Savage brought a diving save from Rovers keeper Danny Coyne in the 25th minute.
Then Coyne was at his best in the 33rd minute when tipping over a power header by Guy Butters which followed a Dean Cox free-kick.
But in the main, Albion created little and they failed to really trouble Coyne throughout the second period.
Butters was excellent in the Albion back four and Dean Cox and Adam El-Abd tried their best in midfield.
Steve Davies was always lively for the winners and Ian Goodison and Shane Sherriff did little wrong in defence.
In the main it was a disappointing game for the fans.
It produced a number of bookings - Greenacre, Steve Jennings and Davies were the Tranmere men cautioned, while Cox of Albion also went in the book along with Whing.
Craig Curran was sent on by Rovers as a 75th minute substitute for Taylor and made an immediate impact with a part in the build-up to the crucial first goal.