When Portugal take on Luxembourg on Sunday, Ronaldo need to score just two more goals to become only the 2nd player in history to reach 100 worldwide goals, only after Iran's legend Ali Daei.
The reigning European champions were made to wait for qualification however as Serbia battled to a 3-2 win over Luxembourg in the other game in Group B.
Portugal are in second place with 14 points, one ahead of Serbia, and will qualify if they win in Luxembourg on Sunday.
"We won. Juventus is in first place, we (Portugal) qualified and I will be 100% fit as fast as possible". Articles appear on euronews.com for a limited time.
Ronaldo's performance came after a turbulent week with his club, after he recently stormed off after being substituted to help rest his knee injury.
Fernandes was brought down by Olivier Thill with 13 minutes left, presenting Ronaldo with a free-kick on the edge of the box, but Portugal's all-time leading goalscorer blazed wide with an effort that looked set to sum up his afternoon.
"I sacrificed myself for the team", he said.
"His match put an end to the doubts about his physical condition, for those who had doubts. Nothing surprises me about Cristiano".
The 34-year-old changed the score-sheet with a cool penalty in the seventh minute before doubling the lead with a long-range strike that sent the stadium into a frenzy.
Lithuania paid for more sloppiness 15 minutes later as they lost the ball in midfield and Paciencia slipped the ball quickly to Ronaldo who produced a wicked, dipping first-time shot which flew past the bemused Setkus from 25 metres. Ronaldo completed his hat trick in the 65th minute with a simple finish.