Yuto Nakamura had given the hosts a shock lead at the Bishan Stadium when he raced through to score on the stroke of halftime, but second-half goals from Shotaro Ihata, Frederic Mendy and Qiu Li helped the Protectors get their continental campaign off to a winning start.
And Lee insists his side weren't just fighting for three points on Wednesday, but also the pride of the S.League after Tampines Rovers had been beaten 3-1 by Kitchee a day earlier.
"After the first half, I told my players to keep the pride of the S.League," Lee revealed at the post-match press conference.
"Tampines lost [on Tuesday], and I think my players upheld the pride of the S.League - that's why I'm so happy. I hope we can keep it up."
Lee admits he did not know much about Citizen ahead of Wednesday's encounter, but was pleased with the way his players managed to adapt and expose their opponents' weaknesses in the second half.
"I was unhappy with our first-half performance because we didn't play well," Lee added. "The opponents had a good plan to counterattack.
"That's why I explained to our guys how to play in the second half.
"When we played in the first half, we only tried attacking down the centre where there was no space.
"We found out our problems during the second half, so I'm happy with the result."
Wednesday's game also marked Citizen's debut in the AFC Cup and coach Chu Kwok Kuen was satisfied with his charges despite the defeat.
"We're satisfied with our overall performance," Chu said. "We had a perfect first half, but in the second half we found it a little difficult since we just arrived two days ago, and there's some difference in the weather and humidity.
"We found that it was difficult for the players to adapt to those things and as a result, Home United outplayed us in the second half.
"This is a very good learning experience for our team because we are relatively inexperienced in terms of continental competition. Compared to our local teams in Hong Kong, Home United are a much a stronger and faster team, so this is a very good experience."
Chu also conceded that Home's physical approach had been too much for his side to handle, but is optimistic they will be able to do better in their next match against Yangon United.
"Defensively, it may be a bit easier for us to prepare [against Yangon] because in today's [Wednesday's] game, we were physically outplayed in the second half by Home United.
"We believe Home United are a much more physical side than Yangon, so we believe [Yangon's threat] will be based on their passing game.
In Group G's other match, Yangon held Thai giants Chonburi to a 1-1 draw.