Shaun Goater gave the table-topping Shrimpers an early lead, but Gary Smith's thunderbolt and Taylor's 78th minute tap-in breathed fresh life into the Dons' bid to avoid the drop.
The Dons started strongly and after Nicky Rizzo's in-swinging free-kick was only half-cleared in the fourth minute, Gareth Edds volleyed a great chance wide from eight yards.
But Southend settled into their passing game and when Smith let Lee Bradbury's low cross slip under his boot in the ninth minute, Freddy Eastwood fired an 18-yard snap-shot inches wide with goalkeeper Ricardo Batista rooted to the spot.
And then Goater capitalised on a defensive error to put the Shrimpers ahead in the 13th minute.
Bradbury robbed Dean Lewington of possession near the byline and crossed for Goater to scuff his 11th goal of the season past Batista from nine yards.
But Smith put the Dons back on terms just three minutes later with a sensational 30-yard screamer.
The 21-year-old midfielder collected the ball outside the box and turned inside one man before unleashing a devastating drive into the top corner with Southend keeper Darryl Flahavan rooted to the spot.
Taylor almost put the fired-up Dons in front in the 23rd minute but after out-muscling stand-in skipper Adam Barrett to Paul Mitchell's long ball, he dragged his effort just wide under pressure from Barrett.
Smith crashed a long range effort just wide as the Dons burst out of the blocks after the break.
But after defender DavePartridge was forced off with a suspected hamstring injury, Southend upped their game and only a terrific block by Trent McClenahan prevented Gower converting Eastwood's low cross at the far post.
Milton Keynes threw on England under-21 striker Izale McLeod and winger Wade Small late on and their arrival heralded an almost immediate impact as Taylor put the Dons 2-1 up in the 78th minute.
Small slotted an incisive ball through to set Smith away on the right of the box and Taylor was there to ram home at the far post from Smith's low cross.