In a statement, Fifa said they had taken into consideration the "sincere remorse" shown by the Argentina head coach, who had flown from Madrid to Zurich after Argentina's 2-1 friendly loss to Spain on Saturday.
But football's governing body warned that a repetition of a similar incident would result in stronger sanctions being imposed in the future.
Fifa had the authority to ban Maradona until after the World Cup quarter-finals, but the 49-year-old was deemed to have breached Article 57 relating to "offensive gestures or language" rather than Article 58, which carries a mandatory five-match stadium ban.
Following Maradona's outburst, Fifa president Sepp Blatter said there was "no alternative" but to ask the governing body's disciplinary committee to open a case.
Maradona, who as a player helped Argentina win the 1986 World Cup, had been under pressure in the build-up to the Uruguay match.
Defeats against Bolivia, Ecuador, Brazil and Paraguay had seriously undermined Argentina's attempts to qualify for South Africa.
Critics questioned Maradona's team selection, with 70 players called up for duty in 14 matches.
And his 13-month tenure has been marked by clashes with players, coaches, journalists and directors.
Less than a week after he took over from Alfio Basile, who resigned in October 2008, there was speculation Maradona would quit following the Argentina Football Association's (AFA) refusal to appoint former captain Oscar Ruggeri as assistant coach.
And influential playmaker Juan Roman Riquelme retired from the international scene, announcing he and the head coach did not live by "the same codes".
Maradona also upset 1986 World Cup-winning coach Carlos Bilardo.
It was envisaged that Bilardo, the AFA's technical director of national teams, would offer support to the inexperienced coach, but Maradona instead said the veteran should "stay up in the directors' box in suit and tie".
Maradona's World Cup highlights
As a player, Maradona produced a series of stellar displays to guide Argentina to victory in the 1986 World Cup and then helped them reach the final, which they lost to Germany, four years later.
But his time as coach has included a 6-1 defeat in Bolivia and a 3-1 home loss to Brazil.
Going into the final two qualifying matches, a poll showed that the majority of Argentina fans thought Maradona was unfit to coach the national team.
But Argentina won both games to book their ticket to South Africa.
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