The on loan Watford forward fired home an excellent individual effort to cancel out Alex MacDonald’s opener for the home-side.
And the striker’s sixth goal of the season proved enough to grab Blues a point, despite substitute Barry Corr being sent off nine minutes from time.
Plymouth shaded the first half and came close to opening the scoring after just four minutes when Guy Madjo’s close range shot was kept out Blues goalkeeper Daniel Bentley.
Moments later, the impressive Onismor Bhasera headed Robbie Williams’ left wing cross wide of the right post before Bhasera’s low effort from 20 yards was smothered by Bentley.
Bhasera then headed wide of the left post from 12 yards before Southend got back in to the game with Elliot Benyon having a powerful shot blocked by the legs of Jake Cole.
Cole then parried out Assombalonga’s header from a Sean Clohessy cross but Plymouth hit back with Guy Madjo dragging a left footed shot wide and Warren Feeney headed inches past the right upright.
However, the Pilgrims were not to be denied for long and they went in front in the 50th minute when Madjo squared the ball to the unmarked MacDonald who drilled a low, 12 yard shot under Bentley’s body and in to the back of the net.
But Blues drew back level just five minutes later when Assombalonga beat Maxime Blanchard with a brilliant piece of skill before running forward and slotting home a neat, right footed shot.
Southend soon throw on both Freddy Eastwood and Corr and the latter almost netted when he just failed to convert a powerful left wing cross from Assombalonga at the far post.
But, in the 81st minute, Corr was sent off after appearing to lash out at Purse.
The dismissal invited pressure back on to Blues but they stood strong to secure a share of the spoils.