United were staring at their first defeat of the season after Blackpool dominated the first half and Charlie Adam corners created headed goals for defender Craig Cathcart and striker DJ Campbell.
United manager Sir Alex Ferguson sent on Ryan Giggs as a substitute and the veteran's influence crushed Blackpool's dreams of a major upset in their biggest game for 40 years when Berbatov volleyed in on 72 minutes and substitute Javier Hernandez equalised with a cool finish.
With Blackpool's players visibly tiring, Berbatov snatched all three points for his side with a clinical strike in the 88th minute to send United five points clear of Arsenal at the top of the table.
"We always have a chance with the spirit we have in the club," Ferguson told ESPN. "We didn't play well in the first half but you know we will always keep going.
"We knew they would get tired in the second half, we kept playing our football and got some more penetration. Ryan gave us composure, Hernandez was a threat with the timing of his runs and Berbatov has been doing that for us all season.
"In the end it doesn't matter how you get the win."
It was a match that felt like a cup tie, such was the obvious disparity between the sides.
The team sheets came out on a simple black and white printout rather than the colourful document produced at Old Trafford.
The stand shook when the fans leaped around in celebration, while Blackpool manager Ian Holloway had said in his programme notes he had to "commandeer the chairman's office because my office is a little too small to be entertaining Sir Alex".
INFERIORITY COMPLEX
Any inferiority complex was quickly put aside after the opener which had fairytale written all over it as Cathcart headed in at the far post against the club where he spent his youth days before being sold to Blackpool in the close season.
Campbell's goal came after another Adam corner was headed on inadvertently by Darron Gibson into the Blackpool striker's path for his sixth goal in his last seven games.
It looked like a major upset was on the cards with United struggling to create any clear chances and apparently on the verge of losing their unbeaten record.
Blackpool were denied what looked like a certain penalty following a clumsy foul by United defender Rafael da Silva and the replacement of Wayne Rooney with Hernandez midway through the second half livened up the visitors' attack.
Berbatov's first strike proved the turning point and Hernandez calmly converted Gigg's fine pass before the Bulgarian's 19th league goal of the season completed the sort of revival that champions are made of.
Rafael was carried off with what looked like a nasty injury following a clash of heads and after he had received lengthy treatment on the pitch, United hung on through 10 minutes of stoppage time to secure only their third away league win of the season.
In the day's other Premier League match, Aston Villa won 2-1 at Wigan Athletic
