He still started 2005–06 with Standard but, on the last day of the August transfer window, signed with Sevilla FC on a 3+1 contract as an immediate replacement for Real Madrid-bound Sergio Ramos.

[6][7] Dragutinović saw regular playing time during his first three seasons, appearing in the middle or the left flank of the back four and scoring once in every campaign as the team won, amongst other trophies, back-to-back UEFA Cups (he took part in a combined 18 matches in those conquests, including the 2007 final against RCD Espanyol).

On 20 February 2010, he netted through an unstoppable curl in a 3–1 victory at RCD Mallorca,[14] precisely the team they edged for the final Champions League berth.

Following a severe injury,[15] Dragutinović's first appearance in 2010–11 only took place on 11 May 2011: he entered the pitch in the last ten minutes of an away fixture against CA Osasuna, with the Andalusians leading 2–0 only to lose 2–3.

On 12 September 2007, in the dying minutes of a UEFA Euro 2008 qualifier in Portugal, Dragutinović was involved in an altercation with opposing manager Luiz Felipe Scolari, whom eventually punched the defender.