The 82nd-ranked Duckworth took the first set 6-3 against his 49th-ranked rival in 43 minutes at Roland Garros on Sunday.
Duckworth then raced out to a 4-1 lead in the second but Diallo - struggling to keep up as his fitness issues deepened - then signalled his withdrawal.
The Canadian had been battling lower back problems leading into the tournament and had reportedly cut a finger on a glass bottle just days before this first-round match.
Duckworth will now meet 29th-ranked Spanish young gun Rafael Jodar or American Aleksandar Kovacevic, who's ranked No.67.
The 34-year-old Duckworth and 24-year-old Diallo each held their serve early in the first set before Duckworth secured the first break - to 15 - to go up 4-2, after Diallo put a backhand into the net under pressure.
Duckworth rode his advantage by holding to love. Diallo held to 15 for 5-3, but the Australian retained his composure to hold to 15 for the first set, before the second set became a procession.
In women's action, Australia's Ajla Tomljanovic threatened a minor upset before going down in a gripping battle with American Caty McNally, 3-6 7-6 (7-5) 6-3.
The 33-year-old Tomljanovic began strongly by holding serve then breaking her 24-year-old rival to love.
But contrasting her composed start, Tomljanovic stumbled when three forehand errors allowed McNally to break back to 15.
A calm hold from the American and another break put McNally up 3-2, before Tomljanovic stormed back.
She broke McNally to love again for 3-3, held to love and broke to 15 to lead 5-3. She then held tough through a lengthy deuce game to take the first set in 48 minutes.
Tomlanovic raced clear early in the second set as McNally failed to win a point in its first two games and was broken to 30 in the third as the Australian led 3-0.
McNally broke back to 30 after an unforced backhand error from Tomljanovic, and after a comfortable hold broke Tomljanovic again to 15 with a forehand winner to tie the set up at 3-3.
Tomljanovic unleashed four winners to break back but dropped serve straight away as McNally took a 5-4 lead.
Both players held serve from there to force a tiebreak, in which McNally gained a decisive mini-break to lead 6-4 before serving out to complete the set in 67 minutes.
McNally carried that momentum into the third set, breaking the faltering Tomljanovic twice for a 3-0 lead, then staving off a break point with a backhand winner to serve out for 4-0.
But Tomljanovic broke back twice to make it 5-3. As a marathon deuce game unfolded, she then saved one match point on serve with a forehand winner, but couldn't save a second after an unforced forehand error.
Thirteen Australians entered the main singles draw at Rolland Garros, seven men and six women.
