With the Potters' safety already guaranteed, their 10th league win of the season at the Britannia Stadium means they approach their final game of the campaign Arsenal next week with a chance of securing a top-half finish.
Wigan will end the season with much less optimism, and the inability to score that is the root of their problems was again apparent here.
Pulis hails Stoke team effort
The Latics had the best of a poor first half with Paul Scharner and debutant Cho Won-hee forcing saves out of Stoke keeper Thomas Sorensen.
At the other end, the closest Stoke came to breaking the deadlock was when one of Rory Delap's trademark throws flew straight into the net without another player managing to get a touch.
The visitors continued to misfire after the break, with Charles N'Zogbia and Lee Cattermole both wasting chances when well placed.
Bruce voices Wigan disappointment
But Stoke eventually came good and Fuller put them ahead when he reached Liam Lawrence's hoisted pass and battled past Emmerson Boyce, Titus Bramble and Maynor Figueroa before firing home.
Beattie added a second seven minutes later when he met Etherington's cross at the far post and headed home.
By now, Wigan boss Steve Bruce had brought Mido off the bench in an attempt to increase his side's attacking threat but it was Stoke who went closest to scoring again before the end when Fuller headed inches wide.
Stoke manager Tony Pulis: "We are absolutely delighted to have won here for the supporters, who have been fantastic.
"It has been a difficult week because after we won at Hull we were safe and the relief of having Premier League football next year takes the edge off.
"We wanted the players to enjoy the week but also have a right crack."
Wigan boss Steve Bruce: "The longer it went on I thought they had the cutting edge and I thought the first goal was always going to win it.
"Overall I didn't think we did enough going forward and we got punished at the other end.
"For too long we've relied on our defensive organisation and when you look at the first goal we've had five attempts to tackle him but Fuller is decent.
"He is the difference and he won them the game today. He kept at it, he was determined, he scored a goal and he was a handful."
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.