Fuller brilliantly netted his tenth of the campaign in the 69th minute and Beattie struck seven minutes later, heading his seventh in 15 starts since a January move from Sheffield United.
The Stoke fans were in party mood for their last home game of a memorable first season in the Premier League.
Tony Pulis' team had defied most punters by securing survival with something to spare and the celebrations began long before kick-off.
Big defender Abdoulaye Faye collected all seven of Stoke's player of the season awards and Pulis received a standing ovation as he jogged to the dugout.
When the action did get underway, Wigan threatened to spoil the party as Paul Scharner's shot from Hugo Rodallega's header drew a fine save from Thomas Sorensen.
And Sorensen was soon in action again when he tipped over a long range effort from South Korea international Won-Hee Cho.
Stoke were struggling to get into their stride as a strong and gusting wind whipped around the Britannia Stadium.
But there was a comical moment in the 32nd minute when one of Rory Delap's jet-propelled long throws sailed straight into the back of the Wigan net.
A goal-kick was the decision of referee Lee Probert as the ball failed to make contact with any player before flying past visiting keeper Richard Kingson.
Pulis made his first substitution at half-time, with Danny Pugh replacing Leon Cort and positional changes for Ryan Shawcross and Andy Wilkinson.
Stoke finally began to build up a head of steam with Glenn Whelan orchestrating from midfield and Liam Lawrence delivering some dangerous crosses.
Wigan still carried a threat on the break as Charles N'Zogbia wasted one chance and Maynor Figueroa fired narrowly wide from another.
But Fuller broke the deadlock when he twisted and turned past several challenges before whipping a right-foot shot into the top right-hand corner of Kingson's net.
The goal knocked the stuffing out of Wigan and Beattie nodded an easy second after Matthew Etherington beat Kingson to the ball on the edge of the penalty area.