Williams said the back problem affected her game earlier this week. She said she will be ready for the French Open, which starts in a week.
"It was feeling a little stiff and I don't think this is the right moment to force (it)," she said. "I just want to relax and get ready for the next few months.
"This is a good week to get better, and I'm confident that I'll be 100 percent."
Sharapova controlled the match with aggressive baseline play, leading 27-9 in winners while committing one fewer unforced error than her 12th-seeded opponent.
"It feels good coming back to the place where you have accomplished so much and to be in the position to regain that position," Sharapova said. "I'm happy how I've progressed."
Sharapova has won three of her last five titles on clay, beating top-ranked Victoria Azarenka in the Stuttgart final last month to add to her titles in Rome last year and Strasbourg the year before. The French Open remains the only Grand Slam the Russian has yet to win.
"The most important thing is physically feeling stronger on the court and handling longer rallies and I recover better," Sharapova said. "I have improved a lot in that department."
At 24, and just a year younger than Sharapova, Kerber won her first career title at the Paris Indoors this year and took another title in Copenhagen. The German player will break into the top 10 for the first time in her career when WTA rankings are released Monday.
The final Sunday is the fifth for Sharapova this year. She won Stuttgart and finished runner-up at the Australian Open, Indian Wells and Miami.
Na has reached her second final of the 2012 after losing the Sydney championship to Azarenka.
The Chinese player beat Sharapova in last year's semifinals at the French Open. Sharapova won their last meeting in Miami in March.
Williams has enjoyed a 17-match winning streak. She had won consecutive titles in Charleston, S.C., and Madrid. She also has two matches in Fed Cup.
Williams will move up one spot to No. 5 in the rankings Monday.
Several other players are also nursing injuries.
Top-ranked Azarenka withdrew with a right shoulder injury before her third-round match. Wimbledon champion Petra Kvitova was bothered by an abdominal injury during a quarterfinals match against Kerber. The Czech lost in three sets.
Italy's Flavia Pennetta retired with a right wrist injury while trailing Williams 4-0 in the first set Friday.
On the men's side, fourth-ranked Andy Murray skipped last week's Madrid Open with a back problem and said it was still affecting him after a three-set loss to Richard Gasquet in the third round at Italian Open this week.
Information from The Associated Press contributed to this report.