Wilkinson added a further two penalties before Munster scored a late David Wallace try to give a final score of 32-16.
Munster were reduced to fourteen men on two occasions with O'Callaghan and O'Gara receving yellow cards.
Paul O'Connell commenting after Toulon's victory "They did the simple things well and they capitalised on our mistakes. Our own ill discipline didn't help and it's been a theme for us throughout the season."
O'Connell added "It's not the end of an era, with great players coming through, young talent emerging and quality players out injured, I think we're a great side that are just not playing well. We're certainly at a cross roads but we just need to find our away again."
Ronan O'Gara also confirmed that "Munster still have a lot to offer. We have to regroup and hopefully come back better."
"They out played us and fully deserve the chance to go into the quarter finals. The better team won, fair play to Toulon, it's what rugby is all about. We fell short everywhere, we were way off the pace. There's no second chance and it's hugely disappointing for us and our supporters."