On May 28, 2007, Bernier left Tromsø for the German 2. Bundesliga club 1. FC Kaiserslautern, where former Vålerenga I.F. Fotball Kjetil Rekdal was the trainer.

On June 25, 2008, he signed a contract with Danish club FC Nordsjælland. On August 14, 2008, he scored the winning goal in the first leg of a UEFA Cup second qualifying round match versus Scottish club, Queen of the South of Dumfries. Bernier scored the winning goal and his first goal of the 2010 season on November 14 in a 2–1 home win over Lyngby. He ended his season early in May against Copenhagen, following an early substitution it was revealed that he suffered a fracture in his fibula. He played over 90 games in all competitions combined with FC Nordsjaelland, from the summer of 2008 until the summer of 2011, winning the Danish Cup in 2010 and 2011. He was voted Player of the Year in 2010 by the supporters of FC Nordsjaelland.

On August 24, 2011, Bernier signed a one-year contract with Lyngby Boldklub. He made his debut against his former club, in a 4–0 loss to FCN. On October 16, Bernier scored his first goal for the club in a 3–2 loss to Silkeborg IF.

On December 19, 2011, Bernier signed a contract to join Montreal Impact upon their entry at Major League Soccer in 2012. He remained under contract with Lyngby Boldklub while they finished their season. However, he had an out clause that allowed him to leave without a transfer fee to the Impact. Bernier scored his first goal for Montreal in a 2–0 away victory against Sporting Kansas City on May 5, 2012. He was named MLS Player of the Week for Week 13–15 in the 2012 MLS. He was also named MLS Player of the Month for the month of August 2012. Under his captaincy, the Impact reached the CONCACAF Champions League final in 2015 and the MLS Eastern Conference final losing to Toronto FC in 2016. At age 38, he played the final match of his career on October 22, 2017 against the New England Revolution.

He made his senior debut for Canada in a November 2003 friendly match against the Czech Republic. By December 2009, he earned a total of 43 caps, scoring two goals. He reached 50 caps in a friendly against Jamaica on September 9, 2014.

After a two-year absence, Bernier returned to the national team under Octavio Zambrano for a friendly against Curaçao on June 13, 2017. The next month he captained Canada at the 2017 CONCACAF Gold Cup, retiring from the national team after Canada’s elimination in the quarter-finals to Jamaica.

In 2018, a few weeks after his retirement, it was announced that Bernier was named as a U13, U15, U17 and U19 assistant coach at the Montreal Impact Academy.