Bottles were hurled at the visiting team bus by Hammers fans in ugly scenes outside the ground prior to Tuesday night's clash.
West Ham went on to win a dramatic game 3-2 before the club paid an emotional farewell to their home of 112 years.
And Hammers boss Bilic is adamant the crowd trouble did not take the shine off a memorable night.
"The best thing from that night was the 90 minutes of the game," he said.
"It was exceptional
First of all it was a great game of football
We were 1-0 up, 2-1 down, 3-2 up in the last game at the Boleyn Ground, against the biggest club in country
Nothing can overshadow that.
"Of course we are not proud of it but we are not about to be blamed for it
What could we do as a club?
"We apologised, the board and the chairman (David Sullivan) apologised and basically that's all we can do.
"The chairman said we can't connect ourselves with the guys who did it and that's it
Nothing can overshadow what we did on the pitch."
West Ham end their season with a trip to Stoke as they attempt to secure at least sixth place and qualification for the Europa League.
Should they lose, a not entirely unfeasible set of results whereby Southampton fail to beat Crystal Palace and Liverpool win against West Brom, could see the Hammers and the Anfield club finish tied for sixth on points, goal difference and goals scored.
Were that the case, and Liverpool did not qualify for the Champions League by winning their upcoming Europa League final, Premier League rules state there would be a play-off at a neutral ground to determine who finished sixth.
But Bilic says the head-to-head results between the two teams should be used instead of playing a one-off game.
"I don't understand why it's even a possibility," he said
"At the end of the day in most of the countries after goal difference, it should be goals scored, then the two games between you.
"That should be the third part
We beat them away and at home so there shouldn't be a possibility for us to play Liverpool.
"But it's in our hands
If we win we will be sixth, minimum
If Manchester United slip up, possibly fifth
If Manchester City lose 25-0, possibly fourth."
Source : PA
Source: PA