The automaker's Toyota brand replaced the Lexus in the annual survey, which measures the percentage of new vehicle buyers and lessees who replace a vehicle with another from the same brand.
Overall industry customer retention fell slightly to 47.9 percent from 49.6 percent in 2005.
"Declining customer loyalty results from considerable improvements in quality, combined with a plethora of choices for consumers," said Neal Oddes, director of product research and analysis at J.D. Power.
"In some instances, new models, such as those in the rapidly growing crossover segment, can have a significant impact on customer retention for a brand."
Crossover vehicles are car-based SUVs, which are typically more fuel-efficient than the traditional SUV, but roomier than a car.
The Toyota brand topped the survey with a 63.9 percent retention rate.
"Toyota benefits from its reputation for exceeding customer expectations in terms of both short-term and long-term quality, which has helped to maintain the high resale value of its vehicles, as well as to expand its customer base," Oddes said.
Toyota, which has seen its U.S. sales and market share rise steadily all year, is expected to overtake General Motors Corp. (GM) as the world's largest automaker in a year.
Toyota's November U.S. sales rose 16 percent, while Ford Motor Co.'s (F) sales fell 10 percent in the same period. GM's sales rose 6 percent.
Honda Motor Co. Ltd.'s Honda brand retained third place, with 60.3 percent retention.
GM's Cadillac ranks highest among American brands and sixth overall, with a 55.5 percent retention rate.
GM earlier this year said the way its vehicles were perceived lagged quality. The automaker's Chevrolet brand ranked seventh, with a 55.3 percent rate.
Of the 12 brands that ranked above the industry average of 47.9 percent, only three were American, including Fords.
Suzuki achieved the largest gain in customer retention, with a 23 percentage point gain since the study began in 2003.
"Several factors contribute to Suzuki's improving loyalty rates, including improved short- and long-term quality, as well as the introduction of new models with better customer appeal," the study said.
The survey is based on responses from more than 138,000 new vehicle buyers and lessees, of which 82,274 replaced a vehicle that was previously acquired new.