The versatile Thomson, who can play all three of the loose forward positions, has been battling the injury since the All Blacks beat France 37-17 in pool play more than three weeks ago.
His injury compounded New Zealand's selection woes, with captain Richie McCaw battling persistent foot pain while number eight Kieran Read only returned from a high ankle sprain in the All Blacks' final pool game against Canada.
New Zealand coach Graham Henry often had just three fit loose forwards to choose from throughout the tournament with locks Anthony Boric and Sam Whitelock forced to deputise as blindside flankers or at number eight.
"I remember sitting here two weeks ago and saying I was (right), so I have to be a bit careful," Thomson said. "It's coming along well, I trained on it today and it felt pretty good so we'll see how it pulls up over the next few days.
"It's been very frustrating.
"Obviously a World Cup tournament is the highlight of your career and unfortunately it's an injury that fell in the weeks that I would have loved to be out there but I've just got to look after it and stay positive."
The All Blacks name their team on Friday for the final against Marc Lievremont's French team with Thomson - if fit - likely to slot back onto the replacements bench in place of Victor Vito.
Henry is likely to include number eight Read, who showed he was getting back to his best in the semi-final against Australia when he pulled off two monstrous tackles that stopped the Wallabies' attack dead. Read said he was feeling better the more he played.
"I had a great time last week and you just want to be putting your best foot forward and playing your best game," he added.
"If you can do that and hopefully 14 other guys or the 22 guys are playing their best game we're probably going to go pretty close to winning this thing."