Portugal navigated a potentially fraught final fixture with Switzerland, who becomes one of the eight European nations who must fight through the playoffs for a spot in Russia.
The others are Italy, Denmark, Croatia, Sweden, Northern Ireland, Greece and the Republic of Ireland.
Strootman to miss WC qualifiers against Belarus, Sweden
The Swiss can consider themselves unlucky after winning all nine previous qualifiers but must now overcome a two-legged play-off in November to earn a fourth straight World Cup appearance.
Ronaldo, who was injured for the opening qualifying defeat in Basel, returned to the Portuguese line-up after coming off the bench to notch the opening goal in a lacklustre 2-0 win in Andorra on Saturday.
Italy's Belotti to miss WC qualifiers against Macedonia, Albania
US pop star Madonna was among the crowd at the Estadio da Luz which erupted when Djourou inadvertently bundled in a dangerous cross from Eliseu four minutes before the break under heavy pressure from Joao Mario.
Manchester City midfielder Bernardo Silva then exchanged passes with former Monaco team-mate Joao Moutinho, threading through the return pass for an unmarked Andre Silva to poke in at the far post.
"We've never pretended to be the best in the world, but we're capable of going head to head against any opponents," said Portugal coach Fernando Santos.
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