Juan Mata put the Blues two up after the break in hugely controversial circumstances, with Atkinson awarding the goal despite replays showing the Spaniard's shot did not cross the line.
But that slice of luck could not detract from Chelsea's superiority.
Didier Drogba scored his seventh goal at Wembley to put the Blues ahead and, even though an incensed Spurs pulled one back straight after Mata's second through Gareth Bale, a cool finish from Ramires, a blistering 30-yard free-kick from Frank Lampard, and a late fifth from Florent Malouda wrapped up a huge win for the west London club and piled yet more misery on Spurs boss Harry Redknapp.
Many saw Sunday evening's game as an audition for Redknapp at the home of English football, but his team were nowhere near clinical enough and Roberto Di Matteo's deserved the win.
Chelsea, now through to their 11th FA Cup final, raised their game to play like a team used to gracing the Wembley turf while Redknapp's team were wasteful and nervous.
Tottenham, who went in to this game with one win in their last eight league matches, will have no trophy to show for a season that started with so much hope but threatens to end with a big whimper.
Chelsea thoroughly deserved their win and will now go into Wednesday's game against Barcelona rightly full of confidence.
There was no indication this game would end up being a goal-fest during a nervy opening quarter in north London.
Drogba bustled his way past William Gallas to get on the end of a long punt from the back but he horribly mis-hit a volley and Cudicini gathered.
The Chelsea defence then backed off and allowed Scott Parker in, but Lampard put in a crucial block.
Careless defending from Kyle Walker then almost gifted Chelsea the lead. He dallied on the ball and Salomon Kalou took advantage, galloping 40 yards towards goal before finding Mata, but his touch let him down.
The Spurs fans thought their team had the breakthrough nine minutes before half-time when Rafael van der Vaart beat Petr Cech, but John Terry cleared off the line.
Emmanuel Adebayor then missed an easy chance. The former Arsenal striker slipped his marker to get in the path of Van der Vaart's looping cross but he failed to connect and the ball struck a post before bouncing to safety.
Tottenham were instantly made to pay for the mistake as Drogba fired Chelsea ahead in the 43rd minute.
The former Marseille man picked up Lampard's long ball and turned Gallas easily before firing a fierce rising shot past Carlo Cudicini.
Chelsea's second came in the 48th minute, but only in very controversial circumstances.
Ledley King's clearance from David Luiz's header fell in to the path of Mata, whose shot hit King on the line and Benoit Assou-Ekotto then cleared while laying on the turf.
The ball had not crossed the line, but referee Atkinson blew his whistle and awarded the goal, much to the fury of the Spurs players and supporters.
Van der Vaart led the vocal protests, shouting at the referee, while another group of Spurs players surrounded assistant Mick McDonough complaining at the decision.
Atkinson waved away their protests, however, and the goal stood.
Tottenham got themselves back in to the game six minutes later.
Scott Parker's brilliant slide-rule pass sent Adebayor free, he was sent tumbling by Petr Cech and Luiz, but the referee played advantage, allowing Bale to tap in to an empty goal from five yards.
Luiz was hurt in the challenge and was carried off on a stretcher to be replaced by Gary Cahill.
Chelsea almost restored their two-goal cushion on the hour mark when Terry climbed to meet Lampard's corner but Assou-Ekotto cleared off the line.
King headed just wide from Van der Vaart's corner as Spurs looked desperately for an equaliser in the final 20 minutes.
Redknapp looked to Jermain Defoe for inspiration, the England striker replacing Van der Vaart with 15 minutes to go, but the game soon fell to pieces for the men in white.
Ramires latched on to Mata's through-ball after being played onside by Walker and he coolly lifted the ball over the advancing Cudicini.
The Tottenham fans fell silent for the first time and they started leaving in their droves with 10 minutes to go thanks to a brilliant 30-yard free-kick from Lampard which dipped and swerved past Cudicini to make it 4-1.
Florent Malouda replaced Ramires and, worryingly for Di Matteo, Drogba hobbled off to be replaced by Fernando Torres.
Malouda robbed Gallas and wandered unchallenged in to the box, but his looping shot just missed the goal, and Torres at the back post.
Tottenham's frustration boiled over in injury-time when Parker lashed out at John Obi Mikel after the Nigerian kicked the England captain while he was on the floor. Both were booked.
The humiliation was complete moments later when Malouda got on the end of Mata's pass and slid past Cudicini for Chelsea's fifth.