The Brazilian made 156 appearances and scored 41 times since joining the Aquile from Sao Paulo in 2010 but completed a move to the Nerazzurri in January for a fee of €20 million (£16.4m).
Lazio supporters protested the sale, but while president Lotito concedes he was disappointed to see the midfielder leave, he felt he had no option after the 28-year-old refused to sign a new deal with the capital club.
"For a year we showed with strength and conviction that we wanted Hernanes to continue his professional experience with the club," the 56-year-old told Italian daily Il Tempo.
"We always believed in his qualities as a man and as a player. We never had any doubts in offering him the chance to continue with an important contract, which would have made him a leader.
"There was also a buy-out clause included, but after the last attempt with his agent and the player, we couldn't reach a positive conclusion.
"We were forced into a corner by Hernanes' refusal to sign, so simply had to accept Inter's offer to avoid losing him on a free transfer. It was a very painful decision, but inevitable to safeguard the club's finances."
Lotito maintains that the club can be satisfied with their transfer business, after bringing in Helder Postiga and Gael Kakuta on loan following Hernanes' departure, though he had some strong words for the role of agents in football.
"I think €20m for Hernanes is acceptable, as we made a healthy profit on his sale," the president continued.
"However, there is still too much power given to players and not enough to the clubs. Agents can behave extremely negatively and that ends up affecting their clients.
"I am firmly convinced we have a competitive squad with many options in every area of the team. Helder Postiga has a lot of international experience and goes to reinforce the attack. Kakuta has great promise.
"I don't buy players just to make the fans and media happy, but only to continue a serious, healthy and competitive football project."