The Bayern Munich midfielder suffered a serious knee problem which ruled him out of the 2014 tournament, where the defending champions were stunningly eliminated in the group stages.
La Furia Roja sealed their spot as Group G winners with Friday's 3-0 win over Albania, Thiago netting the third to cap a devastating opening 26 minutes in Alicante.
"I'm thrilled about the World Cup because I'd already missed out on one due to injury, but a lot of work still needs to be done," Thiago said.
"It's special because of the work carried out by this national team for the past year and a half, and through sacrifice and hard work, we've qualified earlier than planned."
Despite Thiago's optimism about his fitness after playing the full game against Albania, an MRI scan on Saturday revealed he suffered an ankle sprain. The 26-year-old has been left out of the squad for the final qualifying clash with Israel on Monday and was given permission to leave the Spain camp.
Coach Julen Lopetegui is also without the suspended David Silva and Gerard Pique, who will be spared many of the boos from his own fans following his outspoken support of a referendum for Catalonia's independence.
"It's what Pique runs the risk of. We know that he’s very important for us on the pitch," said national team-mate Isco, scorer of Spain's second against Albania.
"He's been in the Spanish national team for 15 years and shown his commitment, but people are free to whistle and think whatever they want. He took it naturally.
"We've succeeded and now we have another objective. It's difficult to mix politics with football and what Spain's experiencing is a shame."