The visitors looked set to hang on for victory after left-back Ben Coker had given them the lead with a 23rd-minute free-kick.
But after Coker was sent off in the 88th minute, Forrester headed home from a free-kick in the first minute of stoppage time to spare Bury from a fourth straight defeat.
"We started the game really brightly, we were in the ascendancy," said Jepson. "We were pleased, although the final ball could have been better.
"Then we get undone by a sloppy goal which cane from our throw-in. That took the wind out of our sails because we were attacking at will.
"As soon as they got the goal they slowed the game right down, which was frustrating for the players and supporters.
"But the positive thing is we kept going. A few heads were down at half-time because we'd had so much of the ball but we had a rallying call.
"They kept going, they dug in there and they got the point, which could prove to be crucial come the end of the season."
Bury had started strongly, with Tom Soares having a shot turned wide by Southend keeper Dan Bentley.
The visitors replied and although Bury keeper Trevor Carson saved centre-half Mark Phillips' header, Coker curled in a free-kick from a tight angle.
Winger Anthony Straker then caught Nathan Cameron in possession and squared for Freddy Eastwood but his shot was smothered by Carson.
Southend's other winger, Kevan Hurst, volleyed narrowly over just after the break while Eastwood wasted another chance.
As Bury struggled to turn their possession into chances, Will Atkinson fired wide on the break for the Shrimpers.
But Coker was dismissed after being booked twice in eight minutes before Forrester headed home from substitute Jordan Sinnott's free-kick.