The 28-year-old struggled with a nagging groin problem earlier in the campaign and was laid low again by a thigh injury after playing in Real's 1-1 draw at home to Olympique Lyon in the Champions League on March 10, when his side went out of the competition.
Spanish media and fans have suggested that the Brazilian was saving himself for the World Cup finals and questioned whether his injury was as bad as it seemed.
"It is unfair not to believe he has been suffering pain," Pellegrini told a news conference on Friday, after including Kaka for Saturday's game away to Real Zaragoza in La Liga.
"What has been said about him doesn't correspond with his professionalism. As soon as he didn't feel any more pain, he has returned to the squad."
Kaka has yet to win over Real's demanding fans after failing to live up to expectations following his glitzy 67-million-euro transfer from AC Milan last June.
Fans at the Bernabeu chanted Kaka's name throughout the two-and-a-half year tenure of former club president Ramon Calderon, after he had promised to sign the midfielder if he was elected, and then failed to deliver.
Florentino Perez successfully completed the deal on his return to the presidency last summer, but Kaka has been put firmly in the shade by his new team mate Cristiano Ronaldo.
Kaka has five games left to win back the Madrid fans and perhaps help them overhaul leaders Barcelona to win the league title, Real's last chance for silverware this season, before heading off to South Africa.
