Benegas played for Vicov and Boca Juniors in his youth career.[3] He first played for Boca's senior squad during the 2016 Argentine Primera División season, making his debut in a defeat to Argentinos Juniors.[1][4] He subsequently participated in Boca's final three fixtures of the season.[1]
In July 2016, Benegas joined fellow Primera División outfit Quilmes on loan.[5] His Quilmes debut came on 10 September against Huracán. In his third appearance, Benegas scored his first career goal versus Olimpo.[1]
After five goals in twenty-seven matches for Brown, Benegas moved across the second tier to Defensores de Belgrano.[1] He scored five times in the curtailed 2019–20, including twice against former club Quilmes.[1]
On 18 February 2021, Benegas headed to South Korea to join K League 2 side Seoul E-Land FC; penning terms until 2023.[7] There was also an offer from an unnamed Spanish club, though he chose the Korean team out of sincerity.[7] He debuted on 28 February in a win against Busan IPark, coming off the bench to replace Lee Geon-hui.[1] He then netted twice on his second appearance against Gimcheon Sangmu on 6 March.[1] After a spell at Paraguayan club Sol de América in early 2022, Benegas returned to his former club, Defensores de Belgrano, on 3 June 2022.[8]