All Black coach Graham Henry said Afoa suffered "a bit of a tweak in the knee" and could be doubtful for the year's final Bledisloe Cup test against Australia in Hong Kong on November 1.
"I don't think it's too serious but he maybe might be a question mark for Hong Kong," he said.
"We won't know until he wakes up in the morning."
Afoa's injury apart, Henry said the hit-out against the Barbarians, who comprised players mainly from the Auckland, North Harbour and Northland unions, was just what his squad needed.
"Our guys were rusty and they needed a game," he said.
"If we hadn't had that game, I think we would have been in trouble in Hong Kong."
All 26 players in the squad got a run at Trusts Stadium in Henderson.
First five-eighth Dan Carter, lock Ali Williams and prop Tony Woodcock, who had not played since the Tri-Nations decider against the Wallabies on September 13, completed the full 80 minutes.
Carter operated at second five-eighth, outside Stephen Donald, in the opening spell, before moving back to his customary position after halftime.
Another to stay on the pitch throughout was winger Joe Rokocoko, who hasn't played for the All Blacks this year because of wrist surgery.
Rokocoko scored two of his side's eight tries.
The battle between Tanerau Latimer and Scott Waldrom to be skipper Richie McCaw's back-up at openside flanker ended with honours roughly even.
The pair went head-to-head throughout the match, with each having one half with the Barbarians, who opened the scoring though a Waldrom try.
Henry wasn't giving away who he thought had won the duel.
"It's highly competitive and they both played well," he said.
"We've got a decision to make."
The result of that decision and others will be made clear on Sunday, when the 35-strong All Black party for the five-test six-match end-of-year tour is named.
After Hong Kong, there is a Grand Slam attempt against Scotland, Ireland, Wales and England, as well as a midweek fixture in Ireland against European Cup champions Munster.
Meanwhile, Rokocoko said he was pleased for the opportunity to get his body back into some contact work again.
He felt his form could be better and it had taken him some time to get into the swing of things.
"I'm just happy the body got a few bumps and bruises today," he said.
"This week has been about contact, and this game as well."
All Black Wider Training Group 56 (Joe Rokocoko 2, Richard Kahui 2, Ali Williams, Dan Carter, Tony Woodcock, Rudi Wulf tries; Stephen Donald 4, Carter 4 cons) New Zealand Barbarians (Scott Waldrom, Jamie Helleur tries). Halftime: 28-5.
