The 27-year-old returned from a two-week injury layoff against West Ham in the FA Cup replay in midweek and got on the scoresheet, taking his tally of goals to nine for the season.
That haul is dwarfed by Robin van Persie's 21 strikes so far this term, but Villas-Boas says Rooney's versatility means he is still the main component of United's team.
Speaking to The Mirror, Villas-Boas bemoaned the fact that Rooney has returned from injury in time to face Spurs.
"We’re always very unlucky, as he seems to return just in time for our games," said the Portuguese.The England international was a substitute in Tottenham's 3-2 win at Old Trafford earlier this season.
"We recognize that we had a fantastic first half in that game but he came on in the second, made a difference and created lots of problems for us," Villas-Boas explained.
He added, "But I think he’s a player who makes Man United tick because of his movements and the fact that he always sacrifices himself for the team.
"Also, because of his team spirit, desire to win and his focus. He has overcome some difficult moments in his career but he’s a top quality footballer.”When asked if Rooney and Van Persie were the most daunting strike partnership he has encountered, he said: "I think so.
"For United, Van Persie is a tremendous success. Another transfer with immediate impact, immediate results, immediate return."