Ronaldo struck 34 minutes into Portugal's match with Croatia, giving his team a 2-0 lead. The 39-year-old was emotional after reaching the milestone in Lisbon, converting Nuno Mendes's cross.
The strike, Ronaldo's first since June, extended his record haul of international goals to 131.
Diogo Dalot, who had scored Portugal's first, then conceded an own goal to give Croatia a way back into the game but Ronaldo's goal proved the difference in a 2-1 win.
In Serravalle, San Marino conceded first against Liechtenstein, themselves on a 40-match winless streak, but the goal was ruled out by the VAR (Video Assistant Referee).
Eight minutes into the second half Nicko Sensoli scored and San Marino, a small enclave in Italy, held on to win 1-0.
It was their first win since beating the same opposition in a friendly two decades and 140 matches ago, and only their second ever.
San Marino has a population of 33,000 and covers 61 sq km. Ranked 210th in the world they had lost 196 of their previous 205 matches.
Prior to this their main claim to fame was scoring after eight seconds in a World Cup qualifier against England in 1993, eventually losing 7-1. It is the second-fastest goal in World Cup qualification history.
Elsewhere Poland let slip a 2-0 lead away to Scotland, but clinched the points with a 97th-minute penalty to win 3-2, Spain were held to a goalless draw by Serbia and Denmark beat a Swiss team reduced to nine after Nico Elvedi and Granit Xhaka were sent off 2-0.
There were also wins for Northern Ireland, 2-0 against Luxembourg, Sweden, 3-1 in Azerbaijan where Newcastle striker Alexander Isak scored twice, and Slovakia, 1-0 in Estonia.
Belarus and Bulgaria drew 0-0.
with agencies
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