The Protectors had initially gone behind in the fourth minute after Sho Kamimura put Albirex ahead, but two goals in the space of six minutes midway through the first half from Frederic Mendy and Shotaro Ihata ensured Home went in ahead at the break.
Qiu Li added a third for the hosts from the spot just after the hour mark, and while Kamimura pulled one back for the White Swans, Mendy made sure of the three points when he grabbed his second a minute later.
Speaking after the game, Lee revealed he was pleased with the way his players had controlled the game.
"I am very happy because my team put in a good performance and we got the three points," Lee said in his post-match press conference.
"Sometimes we don't get the result even with a good performance, but today [Sunday] we did that.
"Until the 75th minute, we had a lot of possession and controlled the game. In the last fifteen minutes, they [Albirex] controlled the game because they wanted to score.
"We controlled things in the middle and in attack, even though we conceded two goals, we played well at certain times.
As he has done for much of this season, Lee deployed an adventurous lineup comprising of Mendy, Ihata, Qiu and Indra Sahdan Daud in attack, and he believes their connection with one another helped put Albirex to the sword.
"I'm very happy to watch Mendy, Qiu Li, Ihata and Indra play together," Lee added.
"When you watch their performance, they play without the ball."
The Home tactician even admitted he was more pleased with his players than he had been when they beat Geylang United 7-1 two weeks earlier.
"When we beat Geylang 7-1, I wasn't happy," he revealed. "We didn't play as one.
"Tonight [Sunday] I'm very happy with our performance - this is football, and hopefully we can continue this way."
Albirex coach Koichi Sugiyama was gracious in defeat, praising their opponents and revealing his players would be taking lessons out of the defeat.
"Home have some wonderful players," Sugiyama said. "If we give them space and time, we cannot win.
"It was a good experience today [Sunday] against a wonderful team."
Sunday's result means Albirex have now picked up just a point in their last three games, after winning their first three matches of the season, and have slipped to fifth in the table.
Nonetheless, Sugiyama remains confident Albirex can still challenge for the title.
"We will continue to try and play our brand of football," Sugiyama added. "The league campaign will continue and we will try our best.
"I believe we can still win the league."
Home are next in action on Thursday when they take on defending champions Tampines Rovers, while Albirex have a bye this week.