Rangers' 1-0 defeat in Pamplona and their elimination from the last 16 of the UEFA Cup were overshadowed by fighting which broke out in a section of the Reyno de Navarro Stadium populated by the Ibrox club's supporters and which provoked swift and fierce intervention by the Spanish police.
Bain, who also claimed that the Rangers support had been infiltrated by hooligan groups, criticised Osasuna for the poor segregation in place at the stadium and will ask UEFA to investigate.
European football's governing body are certain to hold an inquiry in any case with their delegate at the match, Emmanouil Mavrokoukoulakis of Greece, expected to lodge his report
Bain said: "It is incredible, it is almost like there are double standards. Judge us by what we do at Ibrox, and the comparison tonight is non-existent. It has come to the point now that Rangers will go back to UEFA. Having been on the end of previous trouble, we will put forward our point that common standards are not applied."
Rangers were fined and warned last season by UEFA after some of their fans were found guilty of discriminatory chanting during both legs of the Champions League tie with Villarreal. Bain, mindful of the consequences of further punishment at the hands of the governing body, made it clear he felt Rangers' genuine travelling fans had been joined by a more sinister group.
"There is a small element in our support, who I wouldn't even call Rangers fans, who were intent on causing trouble. You probably all saw the banners in there tonight," said Bain referring to Union flags with the words 'Inter City Firm' daubed on them. "Because of the complete lack of segregation policy inside that ground tonight, the vast majority of Rangers fans have been intimidated by heavy handed policing. As a club we are disappointed and we will digest what happened when we get back to Glasgow and take it from there. Anything we do will be done through UEFA."
Clearly stung by what they perceived as incompetence on the part of Osasuna, Rangers produced a letter after the game from Marc Timmer, UEFA's head of stadia and security, which was sent to the Spanish club on 12 March warning them that it was their responsibility to implement all measures necessary including an efficient segregation strategy.
Laurence MacIntyre, the Ibrox club's head of security, head of security, said: "We did a lot of preparation and reported our anxieties to UEFA and all the relevant authorities. UEFA appointed a special security officer for the match and also sent a special letter to Osasuna which picked up our concerns.
"It reminded them that, as the home club, it is their responsibility to look after visiting supporters and provide appropriate segregation. What is so disappointing is that there was a distinct lack of segregation.
"It kicked off tonight when they herded the fans to perhaps try and bring them safely to the stadium. What happens then is that people can push forward from the back and those at the front are batoned at random.
"I was in the police force for 30 years and brought up to use your baton as a last resort. If you did so, you used minimum force but there seems to be a culture here in Spain where you use your baton early on and wallop people. It is a matter of fact there were tickets on sale at the ground today. Osasuna have to look at their arrangements for the game."
There was also disappointment for Rangers on the pitch with Pierre Webo scoring the only goal of the game in the 71st minute to give Osasuna a 1-0 win on the night and a 2-1 aggregate victory. Walter Smith, the Rangers manager, conceded his side had not done enough over the two legs to merit a place in the quarter-finals.
"After a poor first leg performance, we hoped to do better in the second leg," Smith said. "In some aspects we did do better, but overall we didn't really construct enough opportunities in the game and only had a few chances. There were not a great deal of opportunities for either side tonight, although Osasuna had the territorial advantage for much of the game."