The Spaniard took off skipper Steven Gerrard and star striker Fernando Torres to make sure they were not ruled out of Tuesday night's must-win Champions League game in France.
Torres was hurt during the match but Benitez claimed he expected the former Atletico Madrid man to be available for a game that will go a long way towards shaping Liverpool's season.
Benitez said: "We were losing 3-1 and we knew it was really difficult so I was trying to protect the key players for the next game.
"We tried to change it with different players with pace and fresh legs. The Champions League is important. Marseille is the target now.
"Torres had a kick on his ankle so was at risk. He will be okay."
Benitez was convinced referee Andre Marriner had blundered when he had to make penalty decisions at either end of the pitch - awarding Reading one that appeared to be outside the box and denying his side two stronger shouts.
He said: "I am not happy with the decisions but we didn't take our chances and that was maybe the key. We should have had two penalties."
Reading manager Steve Coppell was determined to enjoy his side's first success against one of the so-called 'big four' clubs.
And he insisted his players deserved plaudits for their contributions rather than everyone focusing on Liverpool's shortcomings.
He said: "Wins now, because we are not having as many as last year, they are treasured. Any team in the bottom half of the table would say that. We fully intend to enjoy it tonight.
"For our penalty I would say it was more of a penalty than not. It's not fair to say we won a game but it was on a dodgy penalty - they played a crap team because they were looking for Tuesday's game and, PS: Reading played as well."
But Coppell, a boyhood Liverpool fan, made it clear he sympathised with Benitez.
He said: "In terms of priorities of the games this week I would say we were third (Liverpool play Manchester United next weekend).
"I don't want to put words into Rafa's mouth but Marseille has got to be the number-one priority."