Pakhtakor are now on 55 points, one more than Kuruvchi (Bunyodkor) but the AFC Champions League 2008 quarter-finalists have a game against Shurtan in hand.
Bunyodkor will host Iran’s Saipa on Wednesday in the second leg of their AFC Champions League quarter-finals. The first leg ended in a 2-2 stalemate.
Uzbekistan international Alexander Geynrikh opened the scoring for Pakhtakor from the spot at the stroke of half time and Ilhom Suyunov doubled the advantage three minutes from an hour mark.
Umid Isakov (61) and Alexander Stavila (84) levelled the scores for Kyzylkum but an injury time penalty by Geynrikh helped Pakhtakor record their 17th victory.
Third-placed Neftchi, who are 11 points behind the leaders, defeated Andijan 2-1, Mashal sidelined Lokomotive by the same scoreline and UzDongJu lost to Navabhor 1-0.
Three other games ended in draws with Dynamo were held goalless by Metallurg, Sogdiana and AGMK played a 1-1 draw and the match between Nasaf and Bukhara ended in a goalless stalemate.