Referee Carl Berry pointed to the spot in the 86th minute when two Southend defenders slid in on Mustapha Carayol as he prepared to shoot and Harrold hammered the penalty past Cameron Belford to seal the points.
Southend's best chances fell to Freddie Eastwood, who should have done better when heading wide after 56 minutes and the returning striker had another header saved by Scott Bevan.
Rovers created all the decent first-half chances. Harrold might have done better when his weak 20th-minute shot was saved by Belford following good work by Chris Zebroski.
Belford also had to palm a 20-yard shot from Matt Lund around a post and save from Jim Paterson, while Carayol shot over from a Danny Woodards cross.
Elliot Benyon shot wide for Southend as the visitors found in hard to penetrate a well organised home defence.
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