Wilkinson was forced off in the 28th minute after suffering a recurrence of a hamstring injury.
Reigning champions Toulon went on to beat three-time cup winners Leinster in the quarter-final clash at Stade Felix Mayol and will face Munster or Marseille later this month for a place in the final.
Toulon assistant coach Pierre Mignoni said: "Jonny has aggravated the same hamstring as before but it did not look too serious. Hopefully he will be okay and back in one or two weeks but we have to wait and see."
Wilkinson kicked Toulon 6-0 ahead but a catalogue of handling errors allowed Leinster's Jimmy Gopperth to level by half-time.
However, Xavier Chiocci and Drew Mitchell both scored second-half tries while Matt Giteau kicked 10 points to steer the holders through.
Delon Armitage also kicked a penalty while brother Steffon was named man of the match following a dynamic display.