The captain kicked a drop-goal and two penalties and converted tries from centre Matt Giteau and flanker Juan Smith as the French side emulated Leicester and Leinster by becoming European champions for a second successive season.
Wilkinson, 35 today, will retire after Saturday's French Top 14 final against Castres in Paris.
He said after the 23-6 victory over Saracens at the Millennium Stadium: "I can't say how proud I am to be a part of this team. Our season has a week left, but this is something I'll remember forever."
Saracens could only manage two Owen Farrell penalties in reply as Toulon eased towards winning the 19th and last Heineken Cup final before it is succeeded by the European Rugby Champions Cup next term.
Bidding to become the fifth different English club to be crowned European champions, Saracens struck early through a third-minute Farrell penalty.
They were handed a chance to build on their lead when Juan Martin Fernandez Lobbe was shown a yellow card for a high challenge on lock Alistair Hargreaves.
Toulon, though, struck 10 minutes before half-time when a Wilkinson pass freed Giteau, whose kick ahead was superbly gathered by wing Drew Mitchell, and his inside ball sent Giteau over.
Wilkinson kicked the conversion, hoisting Toulon 7-3 ahead. The former England fly-half then landed a trademark drop-goal to increase their lead to 10-3 at the interval.
Toulon finished Saracens off via a second-half move that owed everything to centre Mathieu Bastareaud's surging midfield power.
His approach play resulted in Smith and Fernandez Lobbe linking expertly, before Smith finished off the move.
Wilkinson converted and then kicked a penalty to leave Saracens with no way back as France ended 19 seasons of Heineken Cup rugby as the tournament's dominant nation ahead of England and Ireland.