David Moyes' side laboured in front of goal, as they have done so far season, but managed to eke out victory without a recognised front-line striker.
Three goals in their previous three matches had pointed to a familiar problem for the Toffees.
And on a day when one centre-forward they let go in the summer was the match-winner a few miles up the road in Lancashire, and the one genuine striker they have left departed Goodison Park in a huff before kick-off it seemed they might pay for their lack of bite up front.
Ayegbeni Yakubu, deemed surplus to requirements by Moyes in the summer and allowed to leave for little over £1million, scored twice for Blackburn on his debut against Arsenal.
Louis Saha, he of the perennial injury problems, was left out of the squad again and reacted by venting his frustration on Twitter.
With Tim Cahill now reclassified as a striker by Moyes, who has few other options at the moment, it highlighted how short the resources are.
But the Scot's sides are nothing if determined and after defender Phil Jagielka had equalised Franco di Santo's opener with only the third goal of his four-year Everton career, youngster Apostolos Vellios headed in with six minutes to go before Royston Drenthe poked home deep in injury time.
It made the absence of Saha, who has played just 41 minutes in two substitute appearances this season, immaterial - although Moyes may have something to say about his pre-match comments.
"I am not good enough. Absolutely destroyed," tweeted the Frenchman, who is understood to have left Goodison Park soon after discovering he was not in the squad.
"It's coz I'm confident in my ability that I'm gutted."
Everton had dominated from the off but after Seamus Coleman's stooping header was turned around the post by Ali Al Habsi.
Di Santo's lack of vision squandered Wigan's chance to take an early lead.
Marouane Fellaini's stumble on the halfway line gave the Argentinian a free run at Jagielka but with the unmarked Victor Moses in acres of space to his right the striker blazed a hopelessly optimistic 30-yard shot well wide.
It was a rare chance in a half which the hosts dominated with Tim Cahill being crowded out by Gary Caldwell after Leon Osman's neat reverse pass had sent Leighton Baines racing into the area.
Caldwell was the busiest centre-half as he also kept out Fellaini's close-range effort as Coleman began to enjoy some freedom on the right.
But Moses posed even more of a threat and looked destined to score when he nipped in front of Sylvain Distin only for Tony Hibbert to slide in and knock the ball behind in the 31st minute.
Moyes will have been furious with the way Di Santo was allowed to collect Ben Watson's near-post corner, casually wander back towards the flag before turning inside Osman and firing in a shot which deflected off Hibbert and past Tim Howard for his third goal of the season.
Having previously struggled for goals the Argentinian has now scored more this season than in his previous three-and-a-half years in England.
However, the lead lasted just 97 seconds as Osman's inswinging corner was met by a powerful Cahill header which crashed against the crossbar, rebounding to Jagielka four yards out who nodded home.
Baines, with a free-kick, and Cahill, with a header, both went close as Everton finished the half strongly.
Everton continued to pressure without threatening after the break.
Their lack of a predatory instinct up front was highlighted in the 76th minute when Osman rolled an inviting cross into the six-yard area only to look up and see none of his team-mates had made a run to connect.
Drenthe and fellow loan signing Denis Stracqualursi, making his debut, came on as substitutes and without very little input the game swung in Everton's favour.
When Hibbert whipped over a cross from the right the 19-year-old Vellios rose highest to head into the far corner of the net.
Even then Everton could not relax with Wigan substitute Dave Jones hitting the crossbar from long range.
However, when Drenthe raced through to poke past Al Habsi in the eighth minute of injury time the fans were finally able to celebrate three points at home for the first time since May.