The visitors' former Torquay loanee fired Paul Sturrock's Shrimpers ahead on 10 minutes when he powered a shot through the legs of United keeper Martin Rice from the right side of the penalty area.
Southend surged further ahead against the Gulls with a breakaway goal after Tomlin combined with strike partner Assombalonga to send the youngster away from the halfway line.
Assombalonga doubled his tally in the 44th minute, heading home at the far post from Kevan Hurst's right wing cross. That lead was increased just a minute into the second half when Tomlin ran through to score his second of the game.
Substitute Ryan Jarvis reduced the deficit with a volley in the 52nd minute, four minutes before Torquay skipper Lee Mansell was red carded for a foul on Assombalonga.