Forward Alexis Sanchez and midfielder Arturo Vidal scored the goals that handed Oscar Tabarez's Uruguayans their first defeat in four matches since they finished fourth at the World Cup in South Africa in July.
Uruguay midfielder Walter Gargano was sent off for a second yellow card offence four minutes before half-time in the match at the Monumental in Santiago.
Fans, who have been hoping to persuade Bielsa to change his mind about leaving the Chile job, waved banners and chanted in support for the popular coach who has presided over one of the country's best spells.
Bielsa, who looked visibly moved by the support, took his record with to 28 wins and 15 defeats in 50 matches since his appointment in 2007. He steered Chile to their first World Cup since 1998.
Having signed a new contract after the World Cup until 2015, Bielsa said on the eve of the Chilean federation presidential election on November 4 that he would resign if the man who had brought him in, Harold Mayne-Nicholls, lost - which he did.
Both teams will meet again in Group C at the Copa America in Argentina in July 2011, by which time Chile will have appointed a new coach.
