When he finished his career as a football player, Ouzounidis managed the team of Kappadokes Alexandoupolis (Greek Fourth Division) as head coach.
Unfortunately, his second year at AEL began badly as the team was knocked out in the first qualifying round of the Europa League, and on 22 February 2010, the young coach was sacked because Larissa had found themselves just above the relegation zone.
In December 2014, Ouzounidis was appointed as manager of Panionios, with which he had a high rate of success over two domestic campaigns, having recorded 28 wins and 20 draws in 70 games.
[7] On 10 August 2016, his contract with the club was terminated unilaterally, mainly because of disloyalty issues raised by the board, due to Ouzounidis simultaneously being in talks with Olympiacos over a potential career move.
[7] On 1 December 2016, Ouzounidis agreed upon a one-and-a-half-year contract with Panathinaikos to take over the vacant managerial role at the club, right after the departure of former manager Andrea Stramaccioni.
[9] He was credited with being eager to manage the team despite the chairman Giannis Alafouzos halting the club's funding and imposing radical budget cuts as a means of reducing Panathinaikos' debt.
On 7 May 2018, Ouzounidis announced that he would leave the club after the expiration of his contract, expressing his openness to returning to Panathinaikos in the future under different financial and administrative circumstances.
[10] On 25 May 2018, Ouzounidis was appointed as manager of 2017–18 Greek Superleague champions AEK Athens, on a biennial contract, only hours after the departure of Manolo Jiménez from the club.
On 23 July 2021, Ouzounidis was fired as Universitatea Craiova head coach following a 0-1 loss against Albanian underdogs Laçi in the 2021–22 UEFA Europa Conference League second qualifying round.