Takuma Sato was quickest on his debut for AJ Foyt Racing in the Sebring IndyCar test on Tuesday.
Ex-Formula 1 driver Sato joined American motorsport legend Foyt's team from Rahal Letterman Lanigan over the winter.
He outpaced Ganassi's Scott Dixon by half a tenth of a second.
"The team started with a set-up they knew, and I needed to feel the difference from what I've experienced, and I did feel some differences," Sato said.
"Then we moved on to the testing programme and various set-up changes. They weren't always positive but we learned from the negative changes too.
"I'm happy that we did some good lap times at the end of the day but it is only testing."
Will Power was the fastest Chevrolet-powered driver for Penske in third, followed by Dario Franchitti.
Justin Wilson, who has not yet been officially confirmed with Dale Coyne Racing, completed the top five.
Graham Rahal was ninth fastest as he continued to get up to speed with new team Rahal Letterman Lanigan.
"I think we made some great gains from the morning to the afternoon," said Rahal. "We gained about 0.6s or 0.7s in the afternoon while others didn't gain anything.
"We're not the fastest but we got ourselves in the ballpark by the end of the day. The car, handling-wise, is starting to come to us. I'm really pleased with the progress."
AJ Allmendinger was 12th of the 13 cars present as he re-acclimatised to single-seaters with Penske.
Pos Driver Team/Car Time Gap 1. Takuma Sato Foyt Dallara-Honda 51.947s 2. Scott Dixon Ganassi Dallara-Honda 52.017s + 0.070s 3. Will Power Penske Dallara-Chevy 52.153s + 0.206s 4. Dario Franchitti Ganassi Dallara-Honda 52.322s + 0.375s 5. Justin Wilson Coyne Dallara-Honda 52.327s + 0.380s 6. Tony Kanaan KV Dallara-Chevy 52.381s + 0.434s 7. Helio Castroneves Penske Dallara-Chevy 52.410s + 0.463s 8. Graham Rahal Rahal Dallara-Honda 52.413s + 0.466s 9. Charlie Kimball Ganassi Dallara-Honda 52.439s + 0.492s 10. Simona de Silvestro KV Dallara-Chevy 52.442s + 0.495s 11. Josef Newgarden Fisher Dallara-Honda 52.498s + 0.551s 12. AJ Allmendinger Penske Dallara-Chevy 52.618s + 0.671s 13. Oriol Servia Panther/DRR Dallara-Chevy 52.690s + 0.743s