Canterbury scrum-half Andrew Ellis and Waikato number eight Sione Lauaki were recalled after missing places in the Tri-Nations squad.
Weepu and Flavell were fined $500 for their part in a late-night drinking session in the run up to the 26-12 Bledisloe Cup win over Australia in Auckland Saturday.
Centre Conrad Smith was also fined, but was included having only recently returned to the squad after eye, knee and shoulder injuries curtailed his Super 14 and Tri-Nations campaign.
Brendon Leonard moved ahead of Weepu behind incumbent Byron Kelleher, while Ellis pipped Weepu and Jimmy Cowan to a place.
Richie McCaw will captain a side including former skipper Reuben Thorne and Jerry Collins with several other members seeking to reclaim the World Cup before moving overseas.
Lauaki had a late fitness test on knee injuries before completing his comeback to the squad.
A space has been left for Canterbury prop Greg Somerville to prove his fitness.
Henry stated that a 29-man squad has been named, with one additional player to be added on August 14 - which will be Somerville, if fit.
Somerville missed almost a year of international rugby after sustaining an Achilles injury in South Africa last September but played 80 minutes for Canterbury in a 29-14 win over North Harbour on Saturday.
Henry also mentioned locks Jason Eaton and James Ryan, who were not considered for selection due to injury.
New Zealand, who claimed the first World Cup in 1987, open their campaign against Italy on September 8 in Marseille.
New Zealand World Cup squad: Dan Carter, Jerry Collins, Andrew Ellis, Nick Evans, Carl Hayman, Andrew Hore, Doug Howlett, Chris Jack, Byron Kelleher, Sione Lauaki, Brendon Leonard, Luke McAlister, Richie McCaw, Leon MacDonald, Chris Masoe, Aaron Mauger, Keven Mealamu, Mila Muliaina, Anton Oliver, Keith Robinson, Josevata Rokocoko, Sitiveni Sivivatu, Conrad Smith, Rodney So'oialo, Reuben Thorne, Neemia Tialata, Isaia Toeava, Ali Williams, Tony Woodcock.