Van Niekerk dived over in the corner for Toulon's second try with six minutes remaining.
Jean-Philippe Genevois and Joe van Niekerk scored tries for Toulon who were outclassed for most of the match.
Irish host Toulon in the Heineken Cup this Sunday, having lost their last three Premiership matches.
Ulster would face Perpignan or Toulon in the semi-finals if they were to beat Northampton.
But Toulon soon lost their own star as Wilkinson was helped from the pitch.
Toulon held firm though and were soon back in the ascendancy thanks to Wilkinson's alertness.
Wilkinson's second penalty restored parity before Toulon put together a series of lightning attacks.
But crucially May missed the conversion and Toulon still needed a converted try to draw level.
Boudjellal hopes Henson's arrival will spearhead Toulon towards the knockout stages of the French Championship.
He has overlooked Bath's Butch James, Toulon's Joe van Niekerk and Leinster's CJ van der Linde.
But at Toulon he will rejoin ex-Sale boss Philippe St Andre, who is the club's director of rugby.
The Argentine is expected to link up at Toulon with Philippe Saint-Andre, who signed him for the Sharks.
The Nautile's support ship, the Nadir, will set off from the Mediterranean port of Toulon later in May.
"If I'm playing regularly for Toulon, then I have no doubt Wales will be calling then, " Henson insists.
After 10 weeks out Williams came off the bench and helped the Ospreys seal a 29-17 victory over Toulon.
Toulon lost Jonny Wilkinson to injury but Thomas Sourice's late try ensured a tense finale at the Stade Velodrome.
Further exits cannot be ruled out, particularly given the comments made by Toulon head coach Philippe Saint-Andre on Thursday.
In 1942, the German army entered Toulon and the French fleet anchored there was scuttled by its own crews.
Hook is joining Perpignan, Byrne is heading to Clermont Auvergne and Henson has already moved to Toulon via Saracens.
In this respect, a close reading of Mr Sarkozy's Toulon speech is revealing.
Toulon are one of three debutants in this season's premier European club competition, along with Aironi and Racing Metro 92.
In addition, Anton Oliver (Toulon), Byron Kelleher (Toulouse), Aaron Mauger (Leicester) and Luke McAlister (Sale) are also leaving New Zealand.
Toulon, however, began brighter at a freezing Liberty Stadium and raced into a 14-3 lead inspired by Lamont's ninth-minute try.
But the Blues' win over Toulon in the Amlin final secured a fourth Heineken spot for Wales at Gloucester's expense.
He could also find Sale's most recent ex-boss, Welshman Kingsley Jones, will be part of St Andre's backroom staff at Toulon.
France had sealed their last-eight spot against Germany on Saturday, before they wrapped up a 4-1 victory in Toulon on Sunday.
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"Wilkinson has always been a fierce competitor but he is like a new man since his move to Toulon, " said Ibanez.
They beat Toulon 28-21 in Marseille on Sunday to end a 15-year wait for a Welsh Euro success after trailing 13-6.
The Blues are hardly paupers but their annual budget is dwarfed by the resources poured into Toulon by owner Mourad Boudjellal.
He scored against England Under-21s in March and took the most valuable player award at last month's Toulon International youth tournament.
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