The Scottish striker is out of contract at the end of the season and was told by boss Peter Taylor before the game that he was playing for his future at the club.
But the 33-year-old responded in perfect fashion after being introduced as a half-time substitute and had a big hand in Paul Ifill's winning goal.
Southend were looking to get back to winning ways following their 4-0 thumping at the hands of Sunderland on Saturday.
And they had the better of what was a dull first half with captain Kevin Maher hitting two good efforts in the opening stages as the visitors looked nervy at the back.
Palace were limited only to half-chances, with striker Clinton Morrison, back in the side in-place of Shefki Kuqi, forcing Darryl Flahavan into a rare save.
So it was a much-needed change when Taylor brought on Freedman in place of full-back Danny Butterfield, and he immediately looked to create things.
He teed up Mark Kennedy inside the box on the hour mark with a clever ball, but the Irishman flashed a shot wide.
But it was Palace keeper Gabor Kiraly who was called into action three minutes later when a Mark Gower volley nearly wrong-footed him after a wicked deflection, but he managed to hold on.
However, the visitors were looking more fluid going forward, and a neat move led to the 65th minute winner.
James Scowcroft got the ball on the right and put a teasing cross behind the back four. Freedman was at the back post to force Flahavan into a save, but the rebound fell to Ifill who slotted home for his second Palace goal.
And Palace had Freedman to thank for the turnaround, as he then struck a shot inches wide almost from the kick-off.
Southend started to get desperate in the last 20 minutes, and Jamal Campbell-Ryce flashed a good-looking shot inches over the bar with quarter-of-an-hour left.
But Palace still had the better chances in the final stages, with young substitute Lewis Grabban forcing Flahavan into a good save.
This was only Southend's third defeat in nine games, but it could be enough to condemn them to relegation after a brief revival of late. Palace meanwhile will still harbour hopes of a late run into the play-offs against the odds.