The former Sheffield United defender was part of Everton's first-choice centre-back partnership alongside Joleon Lescott, but that was no bar to Nigeria international Yobo signing a new deal.
Howard, who broke Neville Southall's 13-year-old club record for league clean sheets this season, was also keen to pledge his future to the FA Cup runners-up.
"It's great that three valuable members of the squad have committed themselves to the club for a lengthy period," manager David Moyes told the club's official website.
"Tim, Phil and Joseph have been big players for us over the last few years and it's great news that they will continue to be so for the foreseeable future.
"I have been pleased with the way we've gone about our business.
"We spoke to Phil, Tim and Joseph and we got everything done and dusted efficiently and quietly, which is the way we like things to be done."
Moyes has already stressed he has no plans to sell any players from his squad.
The manager knows he has to strengthen if he is to have any chance of improving on this season's fifth-place finish in the Barclays Premier League.
Everton's playing staff was devastated by serious injuries this year with Jagielka's ruptured knee ligament the last in a long line which saw the seasons of Aiyegbeni Yakubu (Achilles), Mikel Arteta and Victor Anichebe (both knee) ended prematurely.