Scott Dixon and Dario Franchitti put Ganassi at the top of the standings in the second IndyCar practice session at Motegi.
The pair were fastest in their respective segments in the split session, with Franchitti on course to be quickest on combined times until Dixon beat his benchmark by 0.0639sec with a few minutes to go.
2008 race winner Danica Patrick (Andretti Green) and current points leader Ryan Briscoe (Penske), both from the first group, were third and fourth. KV's Mario Moraes was second to Dixon in group two and claimed fifth overall from Newman/Haas/Lanigan's Graham Rahal in the closing moments.
Raphael Matos continued to show strong form for Luczo Dragon in seventh, ahead of morning pacesetter Helio Castroneves (Penske). Foyt's Ryan Hunter-Reay and Newman/Haas/Lanigan's Oriol Servia again filled the top ten.
Patrick was the only Andretti Green driver near the front, with her team-mates Marco Andretti, Tony Kanaan and top local driver Hideki Mutoh down in 12th, 16th and 17th.
The first session was briefly interrupted by moisture on track, and although no rain fell during the 90 minutes, this afternoon's qualifying session has been brought forward by half an hour to 3 p.m. local time in an attempt to get the grid set before forecast rain arrives later on.
Pos Driver Team Time Gap
1. Scott Dixon Ganassi 27.0750s
2. Dario Franchitti Ganassi 27.1389s + 0.0639s
3. Danica Patrick Andretti Green 27.2341s + 0.1591s
4. Ryan Briscoe Penske 27.2603s + 0.1853s
5. Mario Moraes KV 27.3146s + 0.2396s
6. Graham Rahal Newman/Haas/Lanigan 27.3185s + 0.2435s
7. Raphael Matos Luczo Dragon 27.3723s + 0.2973s
8. Helio Castroneves Penske 27.3732s + 0.2982s
9. Ryan Hunter-Reay Foyt 27.3949s + 0.3199s
10. Oriol Servia Newman/Haas/Lanigan 27.4116s + 0.3366s
11. EJ Viso HVM 27.4199s + 0.3449s
12. Marco Andretti Andretti Green 27.4328s + 0.3578s
13. Dan Wheldon Panther 27.4482s + 0.3732s
14. Justin Wilson Coyne 27.4879s + 0.4129s
15. Tomas Scheckter Dreyer & Reinbold 27.4905s + 0.4155s
16. Tony Kanaan Andretti Green 27.4982s + 0.4232s
17. Hideki Mutoh Andretti Green 27.5014s + 0.4264s
18. Ed Carpenter Vision 27.5735s + 0.4985s
19. Roger Yasukawa Dreyer & Reinbold 27.6662s + 0.5912s
20. Kosuke Matsuura Conquest 27.6680s + 0.5930s
21. Mike Conway Dreyer & Reinbold 27.6843s + 0.6093s
22. Robert Doornbos HVM 27.7629s + 0.6879s
23. Stanton Barrett 3G 28.6897s + 1.6147s