The decision came back to haunt Solskjaer as the Red Devils drew 1-1 with the Toffees at Old Trafford.
Ronaldo was clearly unhappy having only played 30 minutes of the game and stormed down the tunnel immediately after the final whistle.
Many have criticised the United boss for leaving out the 36-year-old, with Gabriel Agbonlahor saying it was a 'sackable offence'.
Sir Alex Ferguson was even overheard questioning the decision in a private conversation with Khabib Nurmagomedov.
Former Crystal Palace owner Jordan has been a fierce critic of Solskjaer, but defended the Man United boss saying Ronaldo cannot physically play every game.
He told talkSPORT: "Of course there is an argument to say you will play your best players, but then there is context and an expansion of that conversation.
"If you've got a snippet of what he said - unless you are rotating, unless the opponent is weaker than you, unless we heard the rest of that conversation we can only give it a certain amount of credence.
"I don't argue with the principal of always playing your best players, but the argument cannot be that unless Cristiano Ronaldo plays every second of every minute of every single game, United will turn to the situation and say 'should have played Ronaldo'.
"He didn't play every minute for Juventus last year. He cannot play 60 games, most players can't."
Edinson Cavani came in to take Ronaldo's place and Jordan argued that there was enough talent in Man United's team to beat Everton.
Jordan added: "Of course we are talking about a slob in Cavani who scores 138 goals for PSG in 200 games, 52 goals for Napoli in 69 games.
"A player that was heralded last season coming through the door and I went 'I'm not sure about him' and people said are you mad, have you seen the quality of this player.
"They had enough on that pitch to win that game and it shouldn't all be about Ronaldo.
"The game itself was there to be won and there was enough talent on the pitch to be able to win that game.
"Irrespective of whether it is Ronaldo or not, he is 36 years of age. Whilst he can play at a certain level and score a lot of goals, there are times when he will need to be rotated and need to be rested.
"It is almost unarguable that Ronaldo has to play every single minute of every single game."