Jagielka underwent surgery after picking up the injury in the 2-1 defeat by Manchester City on 25 April and is expected to be back in August.
He appeared on crutches as the team made a lap of the pitch after their final home game of the season against West Ham last weekend.
Together with Nigeria captain Yobo, he has formed part of an Everton defence that has kept 19 clean sheets this season.
Jagielka's form has earned him his own international recognition with the first of his three England caps coming against Trinidad and Tobago last summer.
Yobo first appeared for Everton in 2002 and was eventually signed on a permanent deal for £3.5m from Marseille a year later.
He is likely to stand in for Jagielka for the Wembley showpiece against Chelsea on 30 May.
It had been reported that initial discussions over his new deal had been unpromising, but today's announcement mean he and Jagielka join Joleon Lescott, who signed a four-year deal in March 2008, in committing their long-term futures to the club.
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