The 26-year-old was left out after making a costly mistake in October's Premier League defeat at Chelsea, with several high-profile errors having come before that for club and country.
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"I'm very pleased because I think we made the right decision at the right moment," Pellegrini told reporters. "It was very good for the team and it was very good for Joe Hart, for everyone.
"Hart took it in a good way. He worked hard and came back to his normal [level of] performance."
With the Three Lions' No.1 back in position at club level, the City boss is hopeful that Roy Hodgson's side will benefit at World Cup 2014, declaring his enthusiasm for ensuring his players' success with their national teams.
"For me, it is very important Joe is the best performer in the national team for England," the ex-Malaga boss remarked. "Of course that's very important - and [the same for] Micah Richards, [Joleon] Lescott and every England player we have."