Despite Henri Camara firing Wigan into the lead, Berbatov showed why Tottenham forked out £10.9million for his services when he helped set up Jermain Defoe for the equaliser, scored the crucial second himself on the stroke of half-time and then played in Aaron Lennon for the third.
After guaranteeing qualification for the next phase of the UEFA Cup, Martin Jol will be relieved that his side managed to transform that form back into the Premiership as they look to move into the top half of the table.
Berbatov almost made it a dream start for the home side within the opening 60 seconds when Lennon's cross fell to the Bulgarian striker and he fired a volley straight at Chris Kirkland.
Wigan battled their way back into the game and striker Henri Camara produced a fine save from Paul Robinson diving low down to his left on 14 minutes.
Camara continued to cause problems for the Tottenham defence and shock the home crowd when he broke the deadlock on 25 minutes.
David Wright's cross into the box picked out Lee McCulloch, who beat Pascal Chimbonda in the air and flicked the ball into the path of Camara, who struck a sweet half-foot volley past Robinson into the roof of the net.
Wigan keeper Kirkland made a superb double save just a minute later to keep his side ahead.
Steed Malbranque weaved his way into the area before seeing his low drive turned away by the former Liverpool keeper.
The rebound fell to Defoe, but he was also denied by Kirkland who got down low to his left to deny the England striker.
Tom Huddlestone almost got Tottenham back into the game with a powerful 35-yard shot which flew inches over the bar.
But Tottenham managed to change the course of the game within the space of 90 seconds.
Berbatov picked out his strike partner Defoe on 43 minutes who turned Wigan defender Emmerson Boyce and fired the ball past Kirkland.
And before the Spurs fans had even had a chance to get back in their seats. Tottenham quickly added a second.
Berbatov showed his value once again when he superbly took the ball past Matt Jackson and struck a powerful shot into the top right-hand corner to make it a week to remember for the forward.
Jackson was having a game to forget for Wigan and things almost got even worse on 53 minutes when he nearly turned the ball past his own keeper when he failed to deal with a cross from Berbatov.
Defoe could have added a third for Tottenham on 55 minutes when he raced on to a neat piece of skill from Lennon, but struck his close-range shot just over the bar.
Substitute Emile Heskey was lucky to escape with just a yellow card following a nasty challenge on Michael Dawson.
Robbie Keane should have sealed victory for the home side in injury time when he turned the Wigan defence but curled his shot inches past the post.
But Lennon ensured the home side picked up all three points when he was picked out inside the box by Berbatov and he made no mistake sliding the ball home.