For 2001, Ambrose was signed by Stone Brothers Racing to drive a Ford Falcon AU.
Ambrose stunned the Supercars Championship world when he qualified on pole on debut, at the Australian Grand Prix support race.
He qualified on pole again for round three at Eastern Creek, round nine at Queensland Raceway and round 11, the Bathurst 1000, where he became the first rookie to take pole position since 1987.

Ambrose went on to finish eighth in the championship, winning the Rookie of the Year award.
He won the fourth round of the season, at Hidden Valley Raceway, although he did not win any of the three races in the round.

In 2002, Ambrose started the season winning pole position at Phillip Island before recording his debut race win in the first race.
He eventually finished third in the championship, including winning the final round at Sandown.

With a new Falcon BA, Ambrose gave the Ford team a great start to the 2003 season with victory in the first race of the Clipsal 500.
He followed this up with a third career win at Eastern Creek After 13 rounds in the 2003 V8 Supercar Series, Ambrose was presented with the driver's series trophy, 102 points clear of second place.

In 2004, Ambrose claimed three pole positions and five round wins and went into the final round at Eastern Creek with a virtually unbeatable lead.
In the end he collected his second championship in the opening Saturday night race and then went on to clean-sweep the round in record-breaking style in his Pirtek Falcon.
Teammate Russell Ingall finished second in the championship, giving Stone Brothers Racing a 1–2 Quinella finish.
The late part of the season was highlighted by an altercation between Ambrose and Rick Kelly when Ambrose appeared to have brake-checked Kelly on purpose after a race at the Gold Coast; Ambrose was fined $10,000 for careless driving.

Ambrose won the coveted Barry Sheene Medal in 2003 and 2004.

Ambrose started 2005 with a clean sweep of the opening round in Adelaide.
He remained in the championship lead and was near to winning the championship until Round 10 at the Bathurst 1000 when he was involved in a controversial crash with Greg Murphy approaching The Cutting late in the race.
The two drivers walked out and argued to applause from the fans.
Both of them were infuriated with one another, and shared some heated words after the crash.
Murphy said "He's got an ego problem that we all know about and it reared its ugly head again, and I'm just not going to put up with it".
Ambrose was quoted after the race was finished with his title hopes;
Greg's probably going to blame me, because he tends to blame everyone but himself for these kinds of incidents.
I knew that I was already 99% past him, I gave him a car-length and a half to go two-wide up into The Cutting, and I just got clean wiped out.

— Marcos Ambrose, on a TV Interview after Bathurst 2005
This crash, combined with a poor performance on the Surfers Paradise Street Circuit arguably lost him a third straight title.
He thereafter supported teammate Russell Ingall's title bid successfully, and the two helped Ford and Stone Brothers Racing take the Drivers, Teams, and Manufacturer's championships.
Ambrose finished third in the championship behind Ingall and fellow Ford driver Craig Lowndes.
For 2001, Ambrose was signed by Stone Brothers Racing to drive a Ford Falcon AU. Ambrose stunned the Supercars Championship world when he qualified on pole on debut, at the Australian Grand Prix support race. He qualified on pole again for round three at Eastern Creek, round nine at Queensland Raceway and round 11, the Bathurst 1000, where he became the first rookie to take pole position since 1987.
Ambrose went on to finish eighth in the championship, winning the Rookie of the Year award. He won the fourth round of the season, at Hidden Valley Raceway, although he did not win any of the three races in the round.
In 2002, Ambrose started the season winning pole position at Phillip Island before recording his debut race win in the first race. He eventually finished third in the championship, including winning the final round at Sandown.
With a new Falcon BA, Ambrose gave the Ford team a great start to the 2003 season with victory in the first race of the Clipsal 500. He followed this up with a third career win at Eastern Creek After 13 rounds in the 2003 V8 Supercar Series, Ambrose was presented with the driver's series trophy, 102 points clear of second place.
In 2004, Ambrose claimed three pole positions and five round wins and went into the final round at Eastern Creek with a virtually unbeatable lead. In the end he collected his second championship in the opening Saturday night race and then went on to clean-sweep the round in record-breaking style in his Pirtek Falcon. Teammate Russell Ingall finished second in the championship, giving Stone Brothers Racing a 1–2 Quinella finish. The late part of the season was highlighted by an altercation between Ambrose and Rick Kelly when Ambrose appeared to have brake-checked Kelly on purpose after a race at the Gold Coast; Ambrose was fined $10,000 for careless driving.
Ambrose won the coveted Barry Sheene Medal in 2003 and 2004.
Ambrose started 2005 with a clean sweep of the opening round in Adelaide. He remained in the championship lead and was near to winning the championship until Round 10 at the Bathurst 1000 when he was involved in a controversial crash with Greg Murphy approaching The Cutting late in the race. The two drivers walked out and argued to applause from the fans. Both of them were infuriated with one another, and shared some heated words after the crash. Murphy said "He's got an ego problem that we all know about and it reared its ugly head again, and I'm just not going to put up with it". Ambrose was quoted after the race was finished with his title hopes;
Greg's probably going to blame me, because he tends to blame everyone but himself for these kinds of incidents. I knew that I was already 99% past him, I gave him a car-length and a half to go two-wide up into The Cutting, and I just got clean wiped out.
— Marcos Ambrose, on a TV Interview after Bathurst 2005
This crash, combined with a poor performance on the Surfers Paradise Street Circuit arguably lost him a third straight title. He thereafter supported teammate Russell Ingall's title bid successfully, and the two helped Ford and Stone Brothers Racing take the Drivers, Teams, and Manufacturer's championships. Ambrose finished third in the championship behind Ingall and fellow Ford driver Craig Lowndes.
Marcos Ambrose