Ronaldo stepped up and slotted the ball home to become just the fourth man in history to score goals at four different World Cup finals.
Rubiales was unhappy with the timing and the lack of transparency behind the announcement that Lopetegui will take over as Real Madrid coach next season.
Portugal shocked many on route to claiming the 2016 European Championships in France, and will again be dark horses to go all the way again in Russian Federation to lift their first ever World Cup.
"We played against a favourite team that wants to win the World Cup and we were winning twice during the game".
The second was an ugly bobble on a grounder by Spanish keeper David de Gea that gave Portugal a 2-1 lead heading into the half.
"We nearly made those three points and we managed to draw".
On Portugal's mindset: "We are 23 players and our head coach can only chose 11 to start the game with. We deserved to win, had the game under control, dominated possession".
An increasingly dominant Spain did draw level in the 24th minute, though, with a goal that survived a VAR review. The second was a gift from David De Gea, who pushed his edge-of-the-box snap shot over the goal line, though again, there's something to be said for Ronaldo's alertness on the break that he was there to capitalize on Goncalo Guedes' layoff following Pepe's defensive clearance.
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Until Ronaldo's free-kick, an enthralling game looked set to end in a great result for Spain, who were coached by Fernando Hierro after Lopetegui was sacked by RFEF chief Luis Rubiales on Wednesday. "So exciting. In the current circumstances, I accept this responsibility with courage, it couldn't be any other way, aware that we have a group of staff and players who have been working towards the World Cup for two years".
Initially, Ronaldo stared back at the Manchester United shot-stopper, but then he decided against engaging with him.
"He has had lots of good days".
Remember, Portugal won the Euro 2016 final without Ronaldo, who suffered an injury in the first half of the match.
'There are players for some matches, there are players for every match & there are players for special matches.
"It wasn't an easy situation".
"I've already said it and the decision is quite certain, you never know 100 percent what will happen but when I say something I usually follow through with it", he insisted.
"But when you have the staff and these excellent young professionals it makes your life a lot easier".