Schumacher, nine races into a comeback with Mercedes [ Images ] at the age of 41 and after three seasons out, finished 15th after being forced to wait at the pit lane exit for a red light to change to green while the safety car was deployed.
It was the worst race placing of a 259-race career that has brought the German a record 91 wins and seven titles with Benetton and Ferrari [ Images ], and was all the more painful because he had run as high as third.
"We would like to have clarification about the safety car situation as the red light on the exit from my first pit stop destroyed a race which otherwise would have offered us very good possibilities," Schumacher said.
"Our point of view is that as the safety car had passed the pits without having the cars lined up behind it, there should not have been a red light."
Mercedes motor sport vice-president Norbert Haug agreed. "Michael could have finished quite high today if the red light at the pit exit had not been switched on," he said.
"This happened contrary to our understanding of the rules which say the pit exit remains open until a line has formed behind the safety car."
Ferrari's Alonso, a double world champion hoping to deliver a win for his red-shirted home fans, crossed the line in ninth place but was later promoted to eighth after others picked up penalties.
The Spaniard had been right behind McLaren's [ Images ] Lewis Hamilton [ Images ] when the safety car came out. While the Briton passed it and picked up a drive-through penalty that he took without losing position, Alonso had to stay behind it and lost out.
"The race was ruined by the safety car and everything that followed on from that," Alonso said in a team statement.
"I am disappointed most of all for the thousands of spectators who were here today and saw how the situation was handled.
"I am very bitter about what happened today. I was in third place, a metre behind Hamilton at the moment the safety car came out on track and, at the chequered flag, he was second and I was ninth, even though we had made the same choice of strategy."
Both Mercedes and Ferrari had arrived in Valencia with major upgrades to their cars and both ended up far from where they had hoped to be.
"The outcome of this grand prix leaves us with a very bitter taste," said Ferrari team boss Stefano Domenicali.
"We had everything we needed to clinch a very good result and we have ended up with a handful of points which is even less than we brought home from our worst race a month ago in Turkey.
"I think that the incidents linked to the neutralisation (the safety car procedure) put some questions on the table regarding how to manage situations like this and the eventual penalties linked to them.
"We have to ensure that our sport remains credible in the eyes of those involved and those who follow it, at the track and in front of their TV screens."