The all-rounder has been withdrawn from the rest of the competition in South Africa ahead of Australia's forthcoming test series.
Shane Watson ordered home from Champions League Twenty20 by Cricket Australia over burn-out fears
Concerned the star all-rounder was at risk of burning out for the second year running due to a heavy playing schedule, Cricket Australia general manager/team performance Pat Howard told Watson he must return home after playing just three matches for the Sydney Sixers.
It means Watson, who guided the Sixers to victory over the Chennai Super Kings yesterday, will miss the final group game and the finals, should the Sydney side qualify.
Sixers general manager Stuart Clark is unhappy with the decision, but Clarke fully endorsed Howard's move ahead of home Test series against world number one side South Africa and Sri Lanka.
The skipper said at CA's season launch: "I'm keen for Shane Watson to get his body right so he can perform throughout these Test series.
"Cricket Australia are learning from areas we probably didn't do as well as we wanted to last year.
"Watto didn't play one Test match last summer so we're trying to rectify what we did and give ourselves the best chance of success.
"It's not about the individual player, it's about doing what's best for the team.
"For me playing for Australia would be the main priority and I know Watto pretty well and I'm sure it's the same with him."
As one of the few players representing Australia in all three forms of the game, the in-form Watson has been his country's busiest cricketer over recent months.
But a similar workload last year sidelined him for the entire summer of Tests and CA is desperate to avoid a repeat.
CA boss James Sutherland said Watson's situation was being monitored closely ahead of the Test series with the top-ranked South Africans, which begins on November 9.
Sutherland said he expected the key player to return home this week to give him a rest and possibly have a four-day Sheffield Shield game for New South Wales, before tackling South Africa in the opening Brisbane Test.
"We're concerned about Shane. His injury record is unfortunate and what that tells us is that we need to monitor him and manage him very carefully and we are."
Watson is the only Australian Test player facing a recall from South Africa, with Mike Hussey, Ben Hilfenhaus and Mitchell Starc free to see out the tournament.
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