"I have absolute respect for the work - which is not easy - that the institution and the referees do," he added.
Maradona, 57, felt Geiger should have penalised Harry Kane for a foul on Colombia's Carlos Sanchez instead of awarding the penalty that allowed the England captain to open the scoring just before the hour mark in Moscow.
"Here's a gentleman who decides, a referee who, if you Google him, shouldn't be given a match of this magnitude... Geiger, an American, what a coincidence," Maradona had said on his nightly World Cup show for the Venezuela-based Telesur broadcaster.
Maradona was pictured wearing a Colombia shirt prior to the game and TV images showed him celebrating Yerry Mina's late equaliser.
Fifa said it was "extremely sorry" to read the comments from "a player who has written the history of our game".
"Fifa strongly rebukes the criticism of the performance of the match officials which it considers to have been positive in a tough and highly emotional match," it said.
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