"On this stage a 7-1 away win is an exception. Maybe I'm naive when I think it normally doesn't work like this, but if Zagreb gave the match away they should be punished," De Boer said after a night that consigned Ajax to the Europa League.
"But I think it is hard to find any evidence in this case," he told reporters.
Lyon's victory in Zagreb, coupled with Real Madrid's 3-0 win in Amsterdam, meant the French side upset the odds to leapfrog Ajax and finish second in Group D on goal difference behind the Spaniards to reach the last 16 of Europe's elite competition.
AJAX 'GOALS'
De Boer said he was disappointed that two Ajax 'goals' were ruled offside with TV replays indicating they should have stood.
"That is a bitter taste because with a 2-2 half-time score there wasn't any problem at all. Madrid weren't really determined to win this match," added De Boer.
"I can't blame the referee [Portuguese Manuel De Sousa] for his decisions as he follows his linesman, who should retire in my opinion.
"But we should only blame ourselves as we failed to clinch a point with the chances we created."
The four-times European Cup winners will issue a statement on Wednesday night's Group D matches later on Thursday.
