He has made his debut in full internationals in May 2006 in a friendly against Saudi Arabia, and played 3 matches in Euro 2008 qualifying.

In July 2007, Lombaerts chose a lucrative transfer to the FC Zenit Saint Petersburg in Russia. At that point he quit his studies and chose for a football career. Zenit eventually won its first Russian league title with the 2007 Russian Premier League. At the beginning of 2008, Lombaerts was sidelined for over half a year as the result of a knee injury. He received knee injury in UEFA Cup game against Villarreal CF during the attack that led to the only away goal against the Spanish team. His actions in this game (goal assist by header) later on have been regarded by Zenit fans as one of the most important steps in the subsequent victory in UEFA Cup. In the following games without him, his team won the 2007–08 UEFA Cup and he also missed the 2008 Summer Olympics where Belgium finished fourth.

Lombaerts finally made his return to Zenit on 19 July 2009, coming on in the 71st minute for Aleksei Ionov against Terek Grozny. Even though Zenit were defeated 3-2, Lombaerts described the happiness of taking the pitch again as similar to “a small child’s joy when walking into a shop full of sweets.” He then quickly became a fixture in defense for caretaker Anatoliy Davydov, helping Zenit win six consecutive matches to get back into the title hunt. On 29 November 2009, Lombaerts scored the game-winning goal against rival Spartak Moscow to put Zenit into the 2010-11 UEFA Champions League as third-place team in Russia.

On 5 July 2010, Lombaerts signed a four-year contract to remain with Zenit.

On 26 May 2014, in a pre-World Cup match against Luxembourg, Lombaerts came on as a substitute in the 77th minute for Jan Vertonghen. As Belgium had already made the 6 permitted substitutions, the match was therefore declared invalid on 4 June.

On 24 March 2017, it was announced that after 10 seasons with Zenit, Lombaerts will return to Belgium for 2017–18 season, signing with K.V. Oostende. He played his last, 289th official game for Zenit on 17 May 2017 in a game against FC Krasnodar and was honoured by the club.

On 30 July 2019 it was announced, that the club wanted to terminate his contract in exchange for a severance payment of 300,000 euros and was sent to the B-team. The club was in financial problems after owner Marc Coucke left the club, why they wanted to part ways with Lombaerts and his heavy weighs.