Three months into the 2005–06 season, Eliáš made his first appearance of the season on 3 January 2006, against the Florida Panthers, after missing 39 games due to Hepatitis A, resuming his role as an alternate captain (replacing Alexander Mogilny). He scored eight points in his first four games to help the Devils win his first nine games back with the team. In the first game of the 2006 playoffs, against the New York Rangers, he became the tenth player to score six points in one NHL playoff game, with two goals and four assists. Eliáš' 2006 playoff campaign was spectacular, despite the fact that the Devils were eliminated by the eventual Stanley Cup champions Carolina Hurricanes in the second round. Eliáš recorded 6 goals and 10 assists for an impressive 16 points in just 9 games.
Eliáš was named the Devils' new captain on 5 October 2006, becoming the seventh captain in the team's history. The previous captain of the Devils was defenseman Scott Stevens, now retired. Eliáš became the first European-born captain in the history of the franchise. However, at the start of the 2007–08 season, Eliáš was stripped of the captaincy by incoming head coach Brent Sutter. The Devils named Jamie Langenbrunner his replacement as captain on 5 December 2007.