The Shrimpers saw off bottom-of-the-table Macclesfield with goals from Peter Gilbert and Neil Harris, but Crawley triumphed 1-0 at Accrington, leaving to settle Southend for fourth place.
"It was always asking a lot for us to sneak in to the top three, but we still have a lot to be proud about.
'We've ended the season with 83 points and I think that would've been enough for promotion in the last three or four years.
"It's a fantastic tally and it's just unfortunate that we haven't got up. We were hoping that Accrington might be able to do us a favour and stop Crawley winning and I'm sure they gave it a really good go.
"But the prize of promotion is still there for us through the play-offs. We're going in to them in good form and like I stressed before the game it's important that we don't go into them feeling disappointed. We've had a good season, we've made real progress and we're not finished yet."