Vilanova is due to sign his contract on Friday and then be presented to the media.
"FC Barcelona have come to an agreement with Francesc 'Tito' Vilanova," read a statement on Barcelona's website.
"This season's first team assistant manager will be the head coach of FC Barcelona for two seasons, through June 30, 2014. Vilanova will sign his new contract this Friday on June 15 at 1200."
Guardiola announced in late April that he would step down from his position as coach to take a sabbatical, with the club immediately nominating Vilanova to take over.
Vilanova, who will be the 16th Catalan manager of the club, spent five years as the assistant coach, helping Guardiola during the most successful period in the club's history.
Together they won two Champions League crowns, three La Liga trophies, one Copa del Rey, three Supercopas, two UEFA Super Cups and two FIFA Club World Cups.
However, this season ended in disappointment as they surrendered the league crown to rivals Real Madrid, and were knocked out of the Champions League in the semi-finals by eventual champions Chelsea.
Also today, Barcelona agreed a one-year contract extension with sporting director Andoni Zubizarreta.
The 50-year-old Zubizarreta, whose previous deal was due to expire next summer, is now tied to the Primera Division giants until June 30, 2014. There is also a clause in the agreement that would see the contract extended for an additional two years.
Former Barca and Spain goalkeeper Zubizarreta became sporting director at the Nou Camp in July 2010 after replacing fellow Basque Txiki Begiristain.