Heynckes was included in West Germany's squad for the 1974 FIFA World Cup, which was held in West Germany. Despite his excellent form at club level, however, he spent most of the tournament on the bench as Gerd Müller, the national team's all-time top goalscorer, was used as the starting centre forward by coach Helmut Schön. Heynckes was in the starting line-up for West Germany's opening two fixtures against Chile and Australia but then played no further part due to injury and die Nationalelf won their second World Cup, beating the Netherlands 2–1 in the final at Munich's Olympiastadion. In 2013, Heynckes said of his experience at the 1974 World Cup, "I was in the starting lineup for the German national team competing for the World Cup, but after an injury I was sidelined for the entire final. This was the greatest disappointment of my life, but it spurred me on and became my greatest source of motivation."
Mönchengladbach finished the 1985–86 season in fourth place in the league. In the third-round of the UEFA Cup, Gladbach beat Real Madrid 5–1 at the Rheinstadion. However, a 4–0 loss at the Santiago Bernabéu Stadium in the second leg saw Borussia eliminated on the away goals rule. In 2013, Heynckes described it as "the worst night of my career".
On 16 January 2013, Bayern announced that former Barcelona coach Pep Guardiola would replace Heynckes in July 2013. General manager Uli Hoeneß later stated that it was not Heynckes' decision to leave Bayern at the end of the season and was forced by the club's wish to appoint Guardiola. Though the club's press release announcing Bayern's agreement with Guardiola had claimed Heynckes would be retiring on the expiration of his contract, he stated he would not make a decision on his future until the end of the season.
After returning from the winter break, Bayern only dropped two points in the entire second half of the Bundesliga season, winning 14 consecutive matches from January onwards and being confirmed as champions on 6 April 2013. This was the earliest a team had ever won the Bundesliga, and Bayern broke several other records during the season including; most points in a season (91), highest league winning points margin (25), most wins in a season (29), longest winning streak in a season (14), most clean sheets in a season (21), best goal difference in a season (+80) and fewest goals conceded in a season (18). The team scored in every match and suffered only one defeat.
On 23 February 2013, Heynckes participated in his 1,000th Bundesliga match as player and manager combined, making him the man with the second most appearances in Bundesliga history. On 14 May 2013, he took charge of a Bundesliga match for what he claimed to be the final time. Fittingly, the match was away at Borussia Mönchengladbach, Heynckes' hometown club who he served for over 20 years as a player and coach.
In the Champions League, Bayern faced Barcelona at the semi-final stage, thrashing the favourites 7–0 on aggregate to reach a second successive final. The performance was seen as a display of physical and tactical superiority of Bayern over Barcelona. In the 2013 Champions League final, Heynckes' Bayern defeated Bundesliga rivals Borussia Dortmund 2–1 at Wembley Stadium, making him the fourth manager (after Ernst Happel, Ottmar Hitzfeld and José Mourinho) to win the competition with two clubs.
On 1 June 2013, Heynckes took charge of Bayern for the last time in the 2013 DFB-Pokal final against VfB Stuttgart. Bayern won the match 3–2, becoming the first German club to complete the treble of the domestic league, the domestic cup and the European Cup. Former Bayern and West Germany captain Franz Beckenbauer, who led die Roten to three consecutive European Cup wins in the 1970s, called Heynckes' 2012–13 side "the best Bayern team ever", a view shared by the club's legendary forward Karl-Heinz Rummenigge. He finished with a record of 83 wins, 12 draws, and 14 losses.
On 4 June 2013, Heynckes announced he would not coach a team during the 2013–14 season. On 21 June, in an interview with Der Spiegel, Heynckes said, "After everything that's happened over the past two years, I'm ready for some peace and quiet. After this string of successes, I could transfer to just about any club in Europe. I have a problem with the finality of saying 'never'. But I can assure you that I have no intention of coaching again. I had a worthy ending." He was replaced by Pep Guardiola, who had his first training session on 26 June 2013.