With both sides occupying lofty positions there was little early action as they cancelled each other out.
Tranmere should have opened the scoring when Paul McLaren's free-kick from the right found Shane Sherriff but Steve Collis parried his 14-yard shot.
Southend, who went into the match in third spot, responded with Eric Odhiambo seeing his shot saved by John Achterberg.
The goalkeeper then parried a 30-yard right-foot shot from Nicky Bailey, before Lewis Hunt's cross was headed onto the roof of the goal by Leon Clarke from six yards.
Rovers' Taylor forced a one-handed save from Collis before the Southend defences were breached on 30 minutes.
McLaren's corner from the right was volleyed home from close range by Chorley for his first Tranmere goal since signing from MK Dons in the summer.
The lead lasted 13 minutes before the Shrimpers equalised when another good Hunt cross was met by Adam Barrett who slammed the ball home from eight yards.
The second half started with Achterberg turning a Garry Richards header onto his bar before Rovers retook the lead on 55 minutes.
McLaren's free-kick from the right was headed past Collis by Taylor from eight yards.
Collis then denied Carl Tremarco before Achterberg punched Bailey's effort out for a corner and then parried a Mark Gower attempt.
Tranmere thought they had a third when McLaren teed up skipper Ian Goodison, but Peter Clarke cleared his effort off the line.
The victory stretched Tranmere's unbeaten run to nine games without defeat. Their only loss of the season was on the opening day against Leeds United.