Mark Gower fired a late goal to keep Southend's revival going as his low cross shot ten minutes from time made it just one defeat in nine for Shrimpers.
Rovers, who believed themselves the winners for most of the match, have won only one in the last nine.
Gower, easily the best player on the field, worked hard for his seventh goal of the season which came after he beat sub Christian Edwards inside the left edge of the box.
His low shot gave keeper Kevin Miller little chance as it sped past his left hand.
Southend were now well on top, and were denied a win only by a great save from Miller at the foot of his left-hand post to deny Drewe Broughton.
Rovers enjoyed the rare luxury of an early lead when Paul Tait, after a little bit of ball juggling, lobbed keeper Darryl Flahavan.
It was his ninth goal of a season hindered by a knee operation, but his second in succession as he regains match fitness.
That lead should not have lasted long for a deep cross from Southend's raiding Duncan Jupp caught out the home defence only for Southend's top scorer Leon Constantine to react with an unfocused soft header.
Matthews' failure to stretch to a byline cross from Tait saw Rovers pass up the chance to double their lead.
But an injury to right-back Daniel Boxall, which saw him replaced by Edwards, thrust Rovers game plan into trouble.
Their big failure though was in allowing Gower too much room in which to develop his probes down the left side. With skipper Kevin Maher always ready to try a shot, Southend were in there looking for an equaliser.
Before it came, both keepers found themselves diving to divert free-kicks from just outside the box.