The defeat came after Kiko Femenía was sent off in the 42nd minute, and the Alicante-born coach, whose side now turn their attention to the Conference League qualifying round, insisted the dismissal shaped the entire contest.
"Of course, we came with a lot of enthusiasm, we wanted to get a good result, the sending-off conditioned the match. It shows a lot throughout the championship, because in the first game, when the legs are tight, it does a lot of damage."
Bordalás said he had not been able to review the incident on replay but was adamant Getafe are punished more harshly than their opponents.
"I haven't seen it again, I haven't seen it, but they don't treat us the same way. The match starts and the first foul we get shown yellow, the second one too.
"Davinchi's card, there was one where they grab Satriano, the same thing, they don't treat us the same way and we can't do anything about it. The team kept competing, maybe we were too brave and they scored the second and third."
He also referenced a booking shown to his own bench during the match.
"I had asked the fourth official that it was a play deserving of a card. They were showing us yellow cards very quickly, and if fouls are committed and cards are shown, you have to do it for both teams."
With Getafe already turning to their Conference League play-off, Bordalás moved swiftly to close the book on the Alavés defeat.
"Now we have to close the chapter, focus on the Conference, we have that qualifier where our whole season is at stake. The match is history, and we prepare for Thursday's game. It's an opponent that's already several matchdays into their league, has come through two qualifying rounds, and it isn't going to be easy."
Asked about his message to the dressing room, Bordalás struck a measured tone despite the scale of the defeat: "There have been things that can be improved, it's the first game. It could happen, it wasn't part of the plan because the team started well, that sending-off was a real shame."
Getafe head into the new season having lost several experienced figures from last term's squad, and Bordalás acknowledged the rebuild is still a work in progress.
"Important players have left. Not just Milla, Arambarri, Juan Iglesias. Now we have to think about the squad we have. There have been a lot of changes, everything takes a process, we'll try to make sure the team keeps improving. Nobody likes losing, you have to accept it."
Getafe's Conference League qualifying tie kicks off on Thursday, with a place in the competition's group stage at stake for a club still adjusting to a heavily reshaped squad after a busy summer of departures.