Orient winger JJ Melligan went close when he met Thornton's deep free kick from the left at the far post but saw his shot turn wide by Blues goalkeeper Darryl Flahavan.
Both sides struggled to create opportunities in the blistering heat until Jamal Campbell-Ryce's twenty yard effort was deflected out for a corner.
Mark Gower then laid the ball off to the Blues winger whose angled drive was palmed out by Orient's goalkeeper Stuart Nelson.
Southend took the lead in the 24th minute when Campbell-Ryce released Alan McCormack who crossed to the left where Gower's shot caught Nelson's foot and went in.
Orient equalised on 38 minutes when Thornton rifled his 30 yard free kick into the top right hand corner of the net, beyond Flahavan's dive.
Southend were denied a second goal after 47 minutes when Campbell-Ryce's cross was cleared as far as Gower, whose low 20 yard shot was saved by Nelson.
Summer signing Thornton continued to cause problems for Southend when his shot from distance went inches over Flahavan's crossbar.
The Shrimpers were reduced to ten men after 57 minutes when McCormack was sent off for a second bookable offence after fouling Thornton.
The midfielder nearly rubbed salt into the wounds by kicking the resulting free kick narrowly wide of Flahavan's right post.
Southend fought back and saw a Peter Clarke header cleared off the line and Campbell-Ryce's follow up punched clear by Nelson. But Boyd finally secured the points when he turned in substitute Efe Echanomi's cross from the right at the far post.