Ludogorets, who won their maiden title in May, have 32 points, followed by Levski on 31. CSKA Sofia climbed to third with 25 points after Brazilian striker Michel Platini's double gave them 2-0 win over Beroe Stara Zagora.
Ludogorets, playing in Bulgaria's third division two and a half years ago, are based in Razgrad - a town with a population of less than 35,000 people. However, the club won a remarkable domestic treble last season.
The hosts, unbeaten at their Ludogorets Arena in the league since March, made a bright start and Genchev opened the scoring after 12 minutes, taking advantage of a defensive mistake by Daniel Dimov.
Ilian Yordanov equalised two minutes after the break to revive the 26-times Bulgarian champions' hopes of a first league win over Ludogorets but their joy was short-lived as former Levski midfielder Genchev hit the target again 11 minutes later.
The 31-year-old, who won the title with The Blues in 2002, made it 2-1 with a stunning 30-metre shot that gave keeper Ivaylo Vasilev, deputising for the injured Plamen Iliev, no chance.
"My boys were impressive today, I would say they're fantastic," said Ludogorets coach Ivaylo Petev. "It's a pity that we missed scoring more goals."