2005–2006

Rule changes for the 2005 season required tyres to last an entire race, tipping the overall advantage to teams using Michelins over teams such as Ferrari that relied on Bridgestone tyres. The rule changes were partly in an effort to dent Ferrari's dominance and make the series more interesting. The most notable moment of the early season for Schumacher was his battle with Fernando Alonso in San Marino, where he started 13th and finished only 0.2 seconds behind the Spanish driver. Less than half-way through the season, Schumacher said "I don't think I can count myself in this battle any more. It was like trying to fight with a blunted weapon....

If your weapons are weak you don't have a chance." Schumacher's sole win in 2005 came at the United States Grand Prix. Prior to that race, the Michelin tyres were found to have significant safety issues. When no compromise between the teams and the FIA could be reached, all but the six drivers using Bridgestone tyres dropped out of the race after the formation lap. Schumacher retired in six of the 19 races. He finished the season in third with 62 points, fewer than half the points of world champion Alonso.

2006 became the last season of Schumacher's Ferrari career. After three races, Schumacher had just 11 points and was already 17 points behind Alonso. He won the following two races. His pole position at San Marino was his 66th, breaking Ayrton Senna's 12 year old record.

Schumacher was stripped of pole position at the Monaco Grand Prix and started the race at the back of the grid. This was due to him stopping his car and blocking part of the circuit while Alonso was on his qualifying lap; he still managed to work his way up to 5th place on the notoriously cramped Monaco circuit. By the Canadian Grand Prix, the ninth race of the season, Schumacher was 25 points behind Alonso, but he then won the following three races to reduce his disadvantage to 11. His win at Hockenheim was the last home win for a German as of now. After his victories in Italy (in which Alonso had an engine failure) and China, in which Alonso had tyre problems, Schumacher led in the championship standings for the first time during the season. Although he and Alonso had the same point total, Schumacher was in front because he had won more races.

The Japanese Grand Prix was led by Schumacher with only 16 laps to go, when, for the first time since the 2000 French Grand Prix, Schumacher's car suffered an engine failure. Alonso won the race, giving himself a ten point championship lead. With only one race left in the season, Schumacher could only win the championship if he won the season finale and Alonso scored no points.

Before the Brazilian Grand Prix, Schumacher conceded the title to Alonso. In pre-race ceremonies, football legend Pelé presented a trophy to Schumacher for his years of dedication to Formula One. During the race's qualifying session, Schumacher had the best time of all drivers through the first two sessions; but a fuel pressure problem prevented him from completing a single lap during the third session, forcing him to start the race in tenth position. Early in the race Schumacher moved up to sixth place. However, in overtaking Alonso's teammate, Giancarlo Fisichella, Schumacher experienced a tyre puncture caused by the front wing of Fisichella's car. Schumacher pitted and consequently fell to 19th place, 70 seconds behind teammate and race leader Felipe Massa. Schumacher recovered and overtook both Fisichella and Räikkönen to secure fourth place. His performance was classified in the press as "heroic", an "utterly breath-taking drive", and a "performance that ... sums up his career".