The 44-year-old needed a second round of surgery following an operation to remove a tumour from his saliva glands in November 2011 and assistant coach Jordi Roura had stepped in while Vilanova was out of action.
He wasn't expected to return until mid-January but visited the players in the morning and then took charge of the afternoon training session.
Many of the squad were absent as they are playing for Catalonia in a friendly against Nigeria on Wednesday evening.
"The coach, operated on on December 20, was the main protagonist at this afternoon's training," the La Liga leaders said on their website.
Midfielders Cesc Fabregas and Alex Song had shaken off minor injuries sustained at the end of December and rejoined their team-mates, while Lionel Messi and Adriano had trained later due to delays to their flights back after the Christmas and New Year break, the club added.
Goalkeeper Victor Valdes had pulled out of the Nigeria match because of a foot problem and trained separately from the rest of the squad.
Vilanova began a course of chemotherapy and radiotherapy after his release from hospital on December 22 and club president Sandro Rosell said he would alternate work with his treatment.
He was sidelined for around three weeks after the surgery in 2011 before returning to his job as assistant to Pep Guardiola and then taking over when his close friend stepped down at the end of last season.
Under Vilanova's stewardship, Barca have made a record-breaking unbeaten start to their league campaign and have a nine-point lead over second-placed Atletico Madrid.
Their opening match of 2013 is at home to city rivals Espanyol on Sunday.
