The midfielder, who had been brought on six minutes from time, curled home from distance as the Bundesliga outfit put their 4-2 opening-game defeat to Manchester United behind them.
Simon Rolfes had put the hosts ahead just before the break but Carlos Vela's rebound from his own saved penalty levelled the scores in the second half.
Midfielder Lars Bender was included despite limping off with an ankle injury on Leverkusen's last outing.
The home side started brightly and the game's first opportunity fell to the in-form Stefan Kiessling, who has five goals in seven Bundesliga games this season, but he fired straight at Claudio Bravo after going through one-on-one.
Leverkusen almost went ahead in the 20th minute when Rolfes' strike deflected off Sidney Sam and forced a smart stop from Bravo.
Sociedad created some chances of their own, though, and 12 minutes before the break Elustondo's superb effort was well kept out by Bernd Leno.
But it was Sami Hyypia's men who took the advantage into the interval, Rolfes firing home after his header from Sam's free-kick had been parried by the goalkeeper on the stroke of half-time.
But, after weathering the storm, it was the hosts who prevailed when Hegeler found the top corner with a stunning last-gasp free-kick that marked his side's 100th goal in the competition.
