Hubočan signed for Zenit on 11 February2008 on a three-year contract for €3.8 million, the highest ever paid to a Slovak club. Hubočan is hoped to fill the vacancy in the center of Zenit's defense created by fellow Slovak defender Martin Škrtel being sold to Liverpool. As Zenit's star center-backs Ivica Križanac and Nicolas Lombaerts were still on the injured list, and defenders Kim Dong-Jin and Roman Shirokov were not quite ready to make their comebacks, Hubočan received his first taste of Champions League football against Real Madrid on 30 September 2008. Only having played a total of 11 games for Zenit, it was a rude awakening as he conceded a disastrous own-goal in the 4th minute. Having only played in 22 league games over two seasons, Hubočan was not quite trusted by former head coaches Dick Advocaat and Anatoly Davydov. He finally broke through to the starting eleven in 2010 under Italian Luciano Spalletti, winning the competition for the unfamiliar left back spot over the likes of Michael Lumb and Radek Šírl. Spalletti rated Hubočan as a hot prospect for the future. On 30 September 2010, he scored his first goal for Zenit in a UEFA Europa League match against AEK Athens F.C.
On 7 September 2017, he joined Turkish club Trabzonspor on loan.
International career
Hubočan played his first international match for Slovakia against United Arab Emirates on 11 December 2006. He was a part of Slovakia's squad for the country's first European Championship tournament in 2016. Hubočan announced his national team retirement on 22 February 2019, at age 33 along with another national team defender and captain Martin Škrtel and forward Adam Nemec. The trio shared a farewell game on 13 October 2019 in a friendly against Paraguay, which coincided with a national team return to Tehelné pole, after 10 years. Although Nemec and Škrtel had starred from the start of the game, Hubočan only entered the game symbolically in the 87th minute, due to a sprain. He entered with the game at 1–1. Ironically, this was Hubočan's first international game at the famed Slovakian stadium, home to the national team for a number of years. The game concluded in the same score.
