Laird had been on loan at Roots Hall since October and has agreed an 18-month contract.
The 26-year-old was released from his O's contract on Friday morning and completed his move in time to be available for the FA Cup tie with Brentford.
Laird told Southend's official website: "I've really enjoyed my time here at Southend and I'm delighted to have signed a permanent deal.
"I've got on well with all of the lads who have been fantastic to me during my time here so far. Hopefully I can play a helping hand in getting the club into League One this season."
Laird scored twice in 15 appearances during his loan stay and Southend lost just two of the games he featured in.
Shrimpers' boss Paul Sturrock added: "We're thrilled to have got Marc in because he's been excellent for us since he arrived on loan.
"He brings a lot to the table in midfield and he played a big role in our unbeaten run that we put together.
"He works hard in training, gets on well with all the lads, and most importantly he has been enjoying his football with us. We're delighted to have him with us permanently."