Ronaldo's late header gave Portugal a 1-0 win in Denmark to kickstart their qualifying campaign, but the meeting between Serbia and Albania in the same Group I was abandoned after crowd trouble in Belgrade.
Germany had suffered their first qualifying defeat since 2007 at the weekend, losing 2-0 in Poland in Group D, but the World Cup winners were greeted by a huge fan mosaic at one end of the stadium in Gelsenkirchen which read simply 'Thank You', proving that such a defeat could not overshadow their heroics of July.
Nevertheless, only five of the players who started in the win against Argentina in Rio de Janeiro three months ago lined up at kick-off against Martin O'Neill's men.
Borussia Dortmund's Erik Durm, who went to the World Cup but did not play, smashed a shot off the bar in the first half before a precise Toni Kroos strike in the 71st minute gave Joachim Loew's men the lead.
But Ireland stunned their hosts by equalising in the fourth minute of added time with their first effort on target from veteran defender John O'Shea.
The result means Poland are top of Group D from Ireland on goal difference, with Scotland and Germany three points further back, while Georgia beat Gibraltar 3-0 to record their first points.
"We're all disappointed. I think that was Ireland's only chance of the game and they scored from it," said Loew. "In the last few minutes, we were simply naive."
Ireland's hero O'Shea added: "We have a fantastic spirit, we didn't want to come off having lost with people thinking we just did ok."
In Warsaw, Poland took the lead against Gordon Strachan's side through Krzysztof Maczynski, but Shaun Maloney and Steven Naismith found the net for Scotland, leaving the hosts requiring a magnificent Arkadiusz Milik goal to earn a 2-2 draw in a thrilling match.
"We were brave enough to come here and play with a lot of forwards and a draw was probably the right result," admitted Strachan.
In Copenhagen, Cristiano Ronaldo headed in Ricardo Quaresma's cross in the fifth minute of injury time to score his 51st international goal and give Portugal victory against their Danish hosts in their first competitive game under new coach Fernando Santos.
Ronaldo said: "I want to congratulate the team for always believing. We knew it was going to be a difficult game but we showed confidence right to the end."
Serbia, Albania clash abandoned
Meanwhile, Albania, who won away in Portugal in Group I last month to precipitate the departure of Portuguese coach Paulo Bento, saw their match with Serbia in Belgrade abandoned after trouble started just before half-time with the score goalless.
A drone sporting the Albanian flag was flown over the stadium, sparking fury among Serbian fans and players and leading to clashes between the two teams on the pitch.
Serbian fans hurled smoke bombs and other missiles onto the pitch in protest in a game from which Albanian fans had been barred because of the sensitive relations between the two countries.
Meanwhile, Northern Ireland made it three wins from three in Group F with a remarkable 2-0 victory away to Greece in Piraeus, Jamie Ward and Kyle Lafferty finding the net either side of half-time for Michael O'Neill's side.
The result leaves Claudio Ranieri's Greece side, European champions in 2004, lagging behind with just one point so far, while a brace from Bogdan Stancu gave Romania a 2-0 win in Finland and Adam Szalai's solitary effort handed Hungary a 1-0 triumph in the Faroe Islands.
In England's Group E, Switzerland recorded their first points with a 4-0 victory away to hapless San Marino, with Haris Seferovic scoring twice and Blerim Dzemaili and Xherdan Shaqiri also on target.
The next round of qualifiers will be played over the weekend of November 14 to 16.
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