Barca extended their winning streak at Camp Nou in La Liga to 23 matches with their victory, which came thanks to Neymar's double.
Villarreal played well and scored a deserved equaliser when captain Mateo Musacchio netted a powerful header just after half-time, but Neymar tapped in after sublime work from Cesc Fabregas and Alexis Sanchez to seal his side's win.
The result saw Barcelona extend their lead on rivals Real Madrid, who sit third, to five points after Carlo Ancelotti's side drew 2-2 at Osasuna.
And Martino was delighted with the way in which his side built on their 4-1 Copa del Rey win over Cartagena and 6-1 UEFA Champions League success against Celtic.
"Apart from the game against Atletico Madrid in the Super Cup, where we won a trophy, this is the game that has given me most satisfaction since I took over," the Argentinian said.
"We have achieved a level of consistency in the last three games against Cartagena, Celtic and today that is pleasing.
"It was a great win for the manner in which we played and the quality of opponent we were facing rather than because Madrid had dropped two points."
Neymar's form has come at the right time for Barcelona, who are currently missing star forward Lionel Messi with a hamstring injury.
And although Neymar will miss Barca's next league match against Getafe due to suspension, he will now be free for their clash against title rivals Atletico Madrid in January.
When asked about Messi's absence, Martino said: "You are always going to miss the best player in the world when he is not there.
"I think we would have played even better in these last two games with him."
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