Tony Smith's side followed up a 28-16 win at Wigan on 1 April with a convincing home victory, although they fell behind to Josh Charnley's try.
Daryl Clark, Ben Westwood and Kevin Penny all crossed for the hosts before half-time to forge an 18-4 lead.
Ryan Atkins' brace, Benjamin Jullien and Westwood's second sealed Wire's biggest Super League win over Wigan.
The Warriors, for whom captain John Bateman scored a late consolation, would have gone top themselves with a win but defeat left them third.
Catalans Dragons will join Warrington at the summit on 20 points if they win at Hull on Friday.
The two tightest defences in the division at the start of play held firm until Charnley slid in at the corner after 17 minutes, but Shaun Wane's 150th game as Wigan head coach quickly turned sour as Clark and Westwood, who barged over with his first touch of the game, overturned the deficit.
Warrington, who lost winger Tom Lineham to a head injury early in the first half, saw off a burst of Wigan pressure before Atkins' close-range try stretched the lead to 20 points and his second effectively killed the contest.
The Wolves' half-back pairing of Stefan Ratchford and Kurt Gidley, who extended his contract on Wednesday, played influential roles throughout, with Gidley also landing five of his six attempts at goal.
Former Great Britain international Iestyn Harris, BBC Radio 5 live sports extra
"In the first 20 minutes, Warrington didn't get into their stride. As soon as Ben Westwood came onto the field and gave them some momentum, they didn't look back.
"For 60 minutes they totally dominated Wigan - physically, in ability and for me that little bit of hunger. They really wanted this.
"They've put a statement of intent there - they've put 40 points on Wigan Warriors.
"Wigan are going to get some players back and they are going to come back strong."
Warrington head coach Tony Smith: "The players were terrific tonight, particularly defensively.
"We were outstanding without the ball and really played a physical game, which you have to do when you play Wigan. If you don't, they dominate you.
"I love watching Ben Westwood - he's tough, hard, effective and keeps going. He's doing a great job for us."
Wigan head coach Shaun Wane: "It's not tough to take - they were the better team. Warrington were outstanding.
"For 25 minutes we handled them physically, but we made changes and lost a bit of momentum.
"Their line speed killed us, we found ourselves under pressure and we couldn't get ourselves back into the game."
Warrington: Russell; Penny, R. Evans, Atkins, Lineham; Gidley, Ratchford; Hill, Clark, Sims, Hughes, Currie, Westerman.
Replacements: G. King, Cox, Jullien, Westwood.
Wigan: Sarginson; Charnley, Gelling, Gildart, Tierney; Gregson, Smith; Clubb, Powell, Mossop, Bateman, Isa, Sutton.
Replacements: Williams, Tautai, Burke, Wells.
Referee: Phil Bentham
Warrington Wolves completed a Super League double over Wigan to move two points clear at the top of the table.