Muguruza called her trainer and had medical attention 22 minutes into the match at Rome's Foro Italico, with Svitolina leading 4-1. It was her fourth retirement of the season after Miami, Brisbane and Dubai.
"I want to say a fast recovery to Garbine, she has such a big tournament ahead in Roland Garros," Svitolina told the crowd.
"It's going to be very tough for her and hopefully she will recover very quickly. I am still a little bit shocked."
The WTA said the injury happened as the Spaniard was returning serves while practising before the match, she made a movement and her neck froze. The French Open in Paris starts on May 28.
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Sunday's final will be eighth seed Svitolina's fourth of the year.
Halep had earlier made light of heavy conditions to cruise into the final with a 7-5 6-1 victory over Dutch 15th seed Kiki Bertens.
The Romanian, a winner in Madrid last weekend for the second year in a row, made sure of her first Rome final in an hour and 17 minutes, with the start delayed by half an hour due to overnight rain.
After a hard-fought first set, with Bertens having her chances and saving five set points to hold serve and take it to 4-5 before then breaking Halep, the Romanian broke back and served out cleanly.
She then romped to a 4-0 lead in the second set before Bertens held serve. But there was no holding off Halep, who made only one unforced error in the set and wrapped up the victory as the skies opened again.
"I feel happy we could finish actually," said Halep. "It's really tough to stop because of the rain but here we are, I'm in the final and it's really nice.
"I feel very confident and coming from Madrid with the title makes me stronger on court, also mentally... I feel great and just want to keep playing and why not try to win this title."
(Reporting by Alan Baldwin; Editing by Ken Ferris and Pritha Sarkar)
