Robben scored his side's third goal in a 4-1 win away at Augsburg on Saturday that wrapped up the league with seven games still to play.
Heynckes withdrew the Dutchman – who is out of contract at the end of the season – after 83 minutes, allowing the 34-year-old to receive a rousing ovation from the travelling supporters.
Substitute Ribery had arrived off the bench just prior to the departure of his long-time team-mate, with the Frenchman celebrating his 35th birthday in style in what could yet be his final campaign with the club.
"It was an act of recognition on my part, because these are players that play for FC Bayern for nine and 10 years respectively," said Heynckes, whose side host Sevilla in the second leg of their Champions League quarter-final on Wednesday, having won the first clash 2-1.
"Where does this happen these days? They are both great professionals with outstanding quality, too.
"[They] are as professional as only a few players that I've worked with, so this was a tribute for them both.
"We have to play Champions League on Wednesday, then Monchengladbach at home, then we have to play at Leverkusen on Tuesday and on Saturday we meet Hannover, I think.
"After that, I hope we play the semi-final of the Champions League. That's a lot, so I want us to keep our energy. That's why he [Ribery] didn't play from the beginning."
95 - Only five players have scored more Bundesliga goals since Arjen Robben joined the league in August 2009 than the Dutch winger (95 goals). Maestro.— OptaJohan (@OptaJohan) April 7, 2018
Bayern now lead nearest rivals Schalke by 20 points, an astonishing gap considering they were third in the table when Carlo Ancelotti lost his job in September.
"We turned in a focused performance today, especially after going one down," Robben told the club's official website after the win over Augsburg.
"People from outside always say we have to win the title, but it's up to us to achieve it. There are no presents in the Bundesliga.
"A huge compliment to the team. We have to enjoy it but stay focused on football."