Joining Gary Johnson's side in League One next season are Scunthorpe and Swansea.
The Iron drew 0-0 at Shrewsbury to take second place while Swansea beat Bury 1-0 at Gigg Lane thanks to Adrian Forbes' goal after 26 seconds.
Southend third before kick-off, were the team to lose out as they could only draw 1-1 at the Cods.
Freddy Eastwood cancelled out Michael Reddy's 57th-minute overhead kick for the home side but Swansea¹s win meant they went straight up.
Southend now face the play-offs, where they will be joined by Northampton, Lincoln and Macclesfield.