That's the rules. If you put something to a vote, the vote wins.
Tell the two of them to try convince the other guys it should go through. If they do, then they can resubmit. You can't, as commish, override a veto if the rules say trades are vetoed by vote.
And now these two owners are going to be pissed, and if the guys who voted it down put in a trade they'll veto theirs. This is why trade votes suck. If anything, it should be commish decides after hearing from people who want it vetoed and hearing from the traders. If you read my other posts, I'm against any trade blocking structure. A commish can alway overturn a trade if there's cheating.
Now, all that said, this trade is a complete ripoff. The dude trading Santana has Uggla and he trades Santana to get Kent? And his response is he's punting pitching completely and wants to upgrade his offense? How about a top second baseman then and not Kent? That just doesn't even make any sense at all. You can't win if you punt pitching. So he's essentially admitting he's giving up the season and dumping Santana.
I never veto anything, but if I got a response like that, I would say "call this collusion or not, but I'm calling it vetoed."