"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.
Earlier on Thursday, online betting authority (ARJEL) said in a statement it was looking into the Zagreb-Lyon game, which is routine procedure for every match with a big score.
ARJEL are expected to announce later on Thursday whether there is any evidence of possible match-fixing.
De Boer said he was disappointed that two Ajax 'goals' were ruled offside with TV replays indicating they should have stood.
With Real leading 1-0 Nicolas Lodeiro headed the ball into the net but the linesman raised his flag and did so again minutes later when Miralem Sulejmani deflected a shot from Vurnon Anita into the Madrid goal.
"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.
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