It keeps alive the U.S. record of being the only country to played in every U-17 World Cup since its launch in 1985.
The USA faces Honduras, a 6-0 winner over Cuba, Saturday and then moves into the Concacaf tournament's knockout phase.
McInerney's two goals took his tally to four in two games, a tournament high. (Honduran phenom Antony Lozano had three goals against Cuba.)
McInerney's first goal came after defender Eriq Zavaleta was was pulled down by a Canadian defender in the box on a corner kick.
In the 30th minute, McInerney received the ball from Alex Shinsky just inside the attacking half, took two touches forward, looked up and hit a blast from 30 yards that found the upper corner.
Shinsky, one of two '93 players in the U.S. midfield along with Luis Gil and a recent addition to the starting lineup, was a handful all game on the left wing.
Nine minutes after McInerney's second goal, Sebastian Lleget scored on a header from close range off Gil's cross. It was Gil's third assist of the tournament.
Canada pulled a goal back in the 70th minute on a low shot by Janiel Hoilett past goalkeeper Earl Edwards, but the Americans put the game away in the 85th minute when Joseph Gyau just seconds after entering the game off a scramble in front of the goal.
Canada cut the lead back to two a second time when an errand backpass by Jared Watts allowed Coulton Jackson to score easily.
The USA wins the group with a win or tie against Honduras, which has four point after its win over Cuba and 1-1 tie with Canada. Thursday's results gave Honduras an almost insurmountable advantage over Canada in the tiebreaker (plus-6 vs. minus-2) in the battle for the second spot. Cuba is mathematically eliminated from contention.
The top two teams from Group A join the top two teams from Group B in the semifinals.
April 23 in Tijuana, Mexico
USA 4 Canada 2. Goals: McInerney pen. 2, 30, Lletget 39, Gyau 85; Hoilett 71, Jackson 86.
USA -- Edwards, Polak, Watts, Zavaleta, Kitchen, Shinsky, Duran, Lletget (Martinez, 76), Gil (Gyau, 84), Jerome (Agudelo, 65), McInerney.
Canada -- Causton, Lapointe-Senecal (Jackson, 65), Samain, Augustin, Bassi, Lao (McNicoll, 70), Hoilett, Teibert, Cobby, Maheu, Oumette.
Yellow cards: USA -- Kitchen 18, Shinsky 85.
Referee: Paul Delgadillo (Mexico).