Wilkinson, who kicked all Toulon's points in their 21-15 quarter-final victory over Leicester, landed seven penalties and a drop goal at Twickenham as the big-name, multi-national side set up an all-French final against Clermont Auvergne in Dublin on May 18.
English Premiership leaders Saracens, also seeking a debut final, trailed 12-9 at the break as Owen Farrell kept them in touch but they were punished for a series of errors and wasted the few opportunities they had with wild passes.
"It's been a great event, a great match, to come out top is a real big thing for us," fly-half Wilkinson said.
"It didn't go fantastically well today and many of the things we planned didn't come off but it was about fighting hard and trying to hang in there and that spirit we've got helped us," added Wilkinson, 34 next month, who captained the team once written off as a money-laden retirement home for past-their-best superstars.
The match had been billed as a kicking contest between Wilkinson and Farrell and in the first half there was little between the two.
Wilkinson, the master, slotted all four of his opportunities while the 21-year-old young pretender matched him until missing from long range just before halftime as Toulon turned round 12-9 ahead.
The rugby was dour and with only 25,584 fans rattling around the 80,000-capacity stadium the occasion failed to get anything close to Saturday's memorable afternoon in Montpelier when Clermont held off a fierce late Munster fightback to reach their first final.
Wilkinson added another three pointer soon after the restart but then Toulon flanker Danie Rossouw was unlucky to be sin-binned for a high tackle on Mako Vunipolo.
That was Saracens' chance but after Farrell slotted the resulting penalty, they blew a great opportunity when Kelly Brown's score was ruled out for an awful forward pass by Farrell.
Another Saracens breakdown offence allowed Wilkinson to land his sixth penalty, from inside his own half, as the French side emerged from their period of numerical advantage with a "3-3 draw".
Toulon, growing in confidence, continued to press and Wilkinson refused to leave centre stage as he landed a snap drop-goal five minutes from time to stretch the lead to nine points.
Farrell had done his utmost to charge it down but instead had to settle for a rueful tap on the shoulder from the man he had flattened an instant too late.
"I said 'good hit' and told him it was a bit of a lucky one," Wilkinson said of the moment when the past and present of English rugby became entwined on the Twickenham turf.
Another successful kick soon after took Wilkinson level with Stephen Jones, who held the semi-final penalties record with seven for the Scarlets in their 2000 defeat by Northampton, and set up a mouth-watering final between the top two teams in France.
"Clermont are one hell of a team," Wilkinson said. "It means there's work for us to do and we'll have to pose some difficult questions.
"Like Saracens and Leicester, against Clermont you don't get room to breath but we're excited about it."
It was a dispiriting day for Saracens, who also lost in their only previous semi-final five years ago.
"We made too many errors and with Jonny Wilkinson kicking every penalty it is really difficult," said captain Steve Borthwick.
"But I thought we worked very hard and I'm proud of them. You make mistakes against a quality side like Toulon and you get punished."