Ivanović again displayed his recent goal-poaching prowess and opened his goalscoring account for the calendar year on 5 January 2013, adding a third goal to the scoreline in a third round FA Cup victory against Southampton. This was also the Serb's first ever goal in the FA Cup. In Paolo Di Canio's debut as Sunderland manager on 7 April, Ivanović divereted David Luiz's long range shot past the outstretched arms of Black Cats goalkeeper Simon Mignolet, securing a 2–1 victory for Chelsea.
In the Europa League Final on 15 May 2013, Ivanović headed in the winning goal in the third minute of second-half stoppage time to give Chelsea a 2–1 victory over Benfica. The goal was the Serb's eighth of the campaign in all competitions, and first in the Europa League, and secured a second successive European title for the London club and the 11th major trophy of the Roman Abramovich era. The win also meant that for ten days, the Blues would hold both the Champions League and Europa League titles at the same time, until the final of the 2013 Champions League final on 25 May. Because of Ivanović's heroic performance at both ends of the pitch, the Serbian defender was named the Man of the Match. Following the match, teammate Frank Lampard lauded Ivanović and described him as a "great man" and added, "You only have to look at him to see what a beast he is, he goes under the radar a bit because he just does his job, but what a player... He has been an absolute professional and he is a man you want on your side."
Ivanović was subject to an oral assault by Liverpool striker Luis Suárez in their Premier League fixture on 21 April 2013. The game ended in a 2–2 draw after Suárez scored a 97th-minute equaliser to salvage a draw. Replays showed that as the two tussled for an incoming cross from Steven Gerrard, which was deflected out by Ryan Bertrand for a corner, Suárez dug his teeth into the right arm of Ivanović. Suárez was found guilty of violent conduct and was handed a ten-match ban for the assault from the FA, but Ivanović did not press formal charges following the match. He initially did not accept the apology from Suárez but afterwards the defender said he calmed down and accepted it.
Ivanović became an integral part of newly appointed Chelsea manager José Mourinho's plans as he started almost all games, missing just one league game so far due to an injury he sustained in the 2–1 win against Liverpool at Stamford Bridge. He made his first appearance of the season at Stamford Bridge on 18 August 2013, helping his side keep a clean sheet with a 2–0 defeat of Hull City. He scored his first goal of the season three days later, heading in Chelsea's winning goal in a 2–1 league defeat of Aston Villa. Ivanović scored the only goal of Chelsea's away victory over title rivals Manchester City on 3 February 2014, bringing the sides level on points through 24 league matches.