Ramos has been football's supervillain number 1 after his role in the injury to Egypt and Liverpool star Mohamed Salah in the Champions League final in May.
Instead of being forced to play Group A winners Uruguay, they now face an easier task against Russian Federation, even with what is expected to be raucous support for the hosts.
But he proved his value to Spain in the second half - first denying Boutaib a second goal with a save at the near post and then punching away a risky ball in the 50th minute as Mbark Boussoufa tried to reach a cross.
It was a defensive mishap that then led Morocco to take a surprise lead, as Sergio Ramos and Iniesta were caught dawdling by Boutaib just inside the Spain half.
Spain's objective at the start of the match was simple: to stay top of Group B. Though already eliminated, Morocco had an objective of their own: to ensure they did not leave the competition goalless.
The 27-year-old has come on for Iniesta in the previous two group games and has impressed in his cameo roles. The Moroccan players could go home with their heads held high. "It's true that at the level they've been playing they deserve more than zero points. We needed them to score on us to force us to react".
Spain didn't have to wait long to get back into the match. "When you look at the lineup it's a mix of Real Madrid and Barcelona so these are outstanding players so our team should be commended".
Defending ruggedly and breaking out in fast counterattacks, Morocco was a constant threat and came close to taking the lead earlier when Noureddine Amrabat rattled the goal frame with a powerful shot in the 55th minute that David De Gea could only watch as it bounced down to safety.
Of course, Morocco entered the match having nothing to play for, but anyone thinking there would be any letup in the Atlas Lions' game would have been quickly disabused of that notion.
Spain are through as group leaders and faces Russian Federation in the round of 16 at the Luzhniki Stadium in Moscow on Sunday (Monday NZ time). A clever sequences of passes saw Diego Costa play Iniesta into the box, and he cut the ball back to a wide-open Isco to fire into the net from seven yards out.
When they regained possession they broke with pace and goal, and almost took the lead after 55 minutes when Noureddine Amrabat's right-foot scorcher from distance cannoned off the crossbar.