This could be a very useful discussion Arkady as many of us have similar questions, though I think you need to give a few details.
Are you definitely comparing like for like? In other words, you say your database on physcial and virtual uses the same storage array, but are the underlying LUNs used for the both of the same performance (i.e. number/speed of disks, RAID level, no other users of them)? Are the physcial servers the same spec (processor generation and clock speed) as the virtual servers and do they both have the same RAM/vRAM (and SGA settings)? Also please describe your benchmarks and the results you have obtained already and how different the TPS and response times are.
Personally I haven't had serious performance issues running on VMware before that weren't related to something else (usually overprovisioned SAN) - I would expect a VM to be a little slower than physical but not drastically so. If you're having problems my initial suspicion is that something outside of the two servers is different.
By the way, I'm only thinking about single instance Oracle db here, not RAC.