The Ospreys centre missed the first half of this season after undergoing a groin operation and still feels some way short of peak condition.
Henson discussed the situation with new Wales coach Gareth Jenkins, and the decision was taken to withdraw him from the squad.
He said: "I need to get my body back into the shape it was before last year's injury.
"I don't feel quite ready for international rugby at the moment, my speed times are down on what they were and I prefer my playing weight to be heavier than it currently is.
"Whilst I obviously don't want to let my team-mates or Wales fans down, I have talked closely with Gareth Jenkins, and the rest of the management team, and we have all agreed that the best thing for me to be doing at the moment is getting my body back into the shape it was before the groin injury last year."
Henson joins fellow senior internationals Martyn Williams, Steven Jones, Robert Sidoli and Michael Owen in being rested for the tour.
The likes of Gareth Thomas, Dwayne Peel, Brent Cockbain and Ryan Jones were all overlooked due to injury.
Wales play their first Tests under Jenkins against Argentina in Puerto Madryn on June 11 and Buenos Aires six days later.
Henson would have proven a valuable member of an inexperienced Wales squad which contained five uncapped players and had an average age of just 24 years, five months.
But Jenkins has made the decision based on the bigger picture and the need to have Henson available and fully fit for next year's World Cup.
Jenkins explained: "It is in the player's best interests to stay at home and work on his conditioning this summer, in order to ensure that he is fully fit for a busy season ahead of the World Cup.
"There is an injury component to deal with - a long-term troublesome groin which needs managing.
"After working closely with Gavin in training this week and talking to him and his regional coaches, we have taken the collective decision that he will be more valuable to us next season after a summer off to work on conditioning and to bring his speed and weight back up to his optimum levels.
"Gavin does not currently feel he is at his 'fighting weight' and we have taken a long-term view of the situation and believe we have reached a conclusion that will benefit both the team and the player in the end."
Jenkins is likely to be add a replacement centre to his squad later this week.