The Swiss climbed to second place in Group E - level on six points with the fourth-placed Lithuanians - with an eventually comfortable victory in St Gallen.
Josip Drmic broke the deadlock in the 66th minute, before Fabian Schar doubled the lead two minutes later.
Fernandes came on as a substitute late on, before Xherdan Shaqiri - who earlier assisted Drmic - struck a late brace.
The Stade Rennais man said getting through Lithuania's defence the first time was the toughest part of their mission.
"We created chances in the first half and we didn't put them away," Fernandes said.
"There was a little anxiety that started creeping in, because in recent matches we had had the same scenario.
"But after we opened the score, there was more space. We scored more goals and I'm happy for the team and happy for our forwards who needed confidence.
"At half-time we had a talk and said to each other that we had to take our opportunities. That's what we did. I think people enjoyed watching the second half. We tried to push, keep the ball and dominate - and in the end we won.
"It was the hardest thing to do to break the deadlock. I think if we'd scored in the first half, it would have been a different game.
"But we won, we scored four goals, and that is what we have to keep in mind. We took three points, we're second in the group and that's important.
Defender Johan Djourou claimed the Swiss were on the upward incline, after four games under Vladimir Petkovic - who took the reins from Ottmar Hitzfeld following the World Cup, after the latter took the nation to the knockout stages in Brazil.
"I think we have improved together, the squad has learned a lot together in the last few years. Our World Cup was promising, we might even have got past Argentina," Djourou said.
"After that, a new coach arrived with a new philosophy and I think it always takes time to adapt.
"But we hope the wheels have now been set in motion and they won't stop. I think we have some good years ahead."
