The 34-year-old striker netted in the seventh minute when he latched onto a pass from debutant centre back Dorian Dervitte and looped the ball over goalkeeper Steve Phillips before heading in from a yard out.
The veteran forward's strike gave the Shrimpers their first league victory since late October.
Both sides desperately needed the points as they battled to avoid being dragged into the relegation dogfight.
Southend started the brighter with on-loan striker Theo Robinson looking dangerous.
He forced Phillips to block with his feet, but the hosts saw their other attempts from Robinson in the first half all go off target.
Bristol Rovers had little joy in front of goal in the opening period with Jeff Hughes driving wide and skipper Stuart Campbell firing over the bar.
Phillips parried a Jean-Francois Christophe effort shortly after the interval before Rickie Lambert, who bagged four in Rovers' 4-2 win over Southend in October, fired straight at Steve Mildenhall.
Freedman then bagged the goal and Phillips was lucky to only receive a yellow card when he handled a shot from the striker outside of his box.
Peter Clarke scored from the resulting free-kick but it was ruled out for offside.
Substitute Darryl Duffy then blew a great chance to equalise for the Pirates when he was one-on-one with Mildenhall, but the keeper blocked the forward's effort with his right foot with five minutes left.