The move gave Alvarez his team-leading 16th quality start of the year but Toronto's bullpen couldn't get him the win as New York rallied for a 9-6 victory at Rogers Centre on Sunday.
With the win, the Yankees' magic number for locking up a playoff spot was trimmed to one. New York (92-67) remained tied with Baltimore atop the American League East after the Orioles beat Boston 6-3.
Toronto (70-89) has been out of the playoff picture for a while and is looking ahead to the 2013 campaign. Alvarez, a regular starter this year in a rotation that has been hamstrung with injuries, looked solid over the last few weeks after a mid-season swoon.
"We've seen a good start, some struggles in the middle and a finish on a positive trend," Farrell said. "He goes into the off-season I would think with a lot of confidence about the way he's pitched late in the season."
Alvarez could be a key cog in the rotation down the road. The right-hander relies primarily on his fastball but his change-up has come around and he hopes to use his slider more next year.
Alvarez allowed seven hits and two earned runs with four strikeouts and no walks. The 22-year-old Venezuelan finished his first full season as a starter with a 9-14 record and 4.85 earned-run average.
"The overall start to finish — going through a full major-league season — is a success in its own right," Farrell said. "And the overall growth based on the challenges he faced."
The Blue Jays staked Alvarez to a four-run lead and he left after giving up one run in the sixth. New York pulled even in the seventh, scored twice in the eighth and added two insurance runs in the ninth.
Reliever Boone Logan (7-2) got two outs for the win as New York (92-67) used a 15-hit attack to salvage a split of the four-game series. Robinson Cano and Derek Jeter had three hits apiece as the Yankees completed their 43rd come-from-behind win of the season.
"With an experienced group you just let them have their at-bats and tell them keep putting up good at-bats and that’s what they did," said New York manager Joe Girardi. "It was an outstanding job on their part."
Eduardo Nunez knocked in the go-ahead run with a sacrifice fly and Jeter followed with an RBI single. In the ninth, reliever Jason Frasor loaded the bases and Curtis Granderson took advantage with a two-run single.
The Blue Jays had the potential tying run at the plate but could only get one run across as Rafael Soriano settled down and got Adam Lind on a grounder to end the game.
Canadian Brett Lawrie hit a two-run homer for the Blue Jays, who had 10 hits on the day.
The Yankees started their comeback in the sixth by scratching out a run. Cano doubled, moved to third on a Nick Swisher single and scored on a wild pitch.
Alvarez struck out Canadian Russell Martin to get out of the jam. Brett Cecil relieved Alvarez in the seventh and was pulled after giving up a single to Nunez.
Blue Jays reliever Steve Delabar didn't fare much better.
He gave up a ground-rule double to Jeter and Ichiro Suzuki knocked in Nunez with a sacrifice fly. After a walk to Alex Rodriguez, Cano cashed in Jeter with a double to make it a one-run game.
Aaron Loup relieved Delabar and threw a wild pitch that brought home Rodriguez with the tying run. The Blue Jays escaped further damage when Swisher lined out to Yunel Escobar at short, who flipped the ball to Lawrie to double off Cano at third base.
Toronto's bullpen continued its struggles in the eighth as reliever Darren Oliver (3-4) walked Granderson and gave up a single to Raul Ibanez.
Brandon Lyon came on and Martin, from Chelsea, Que., dropped down a sacrifice bunt to move the runners ahead. Nunez then stroked a fly ball to centre that brought home Granderson.
The Blue Jays started the game strong, getting to Yankees starter Phil Hughes in the opening inning. Rajai Davis singled, moved to second on a walk to Edwin Encarnacion and scored on an Escobar double.
Encarnacion scored the game's second run on a sacrifice fly by Lind.
Eric Chavez put the Yankees on the board in the third when he took the first pitch from Alvarez over the wall for his 16th homer of the season. New York later put runners on the corners after Lawrie threw wildly to first after snagging a hot shot from Cano.
Lawrie, from Langley, B.C., atoned for the error by tracking down Swisher's slow grounder and throwing him out to preserve the one-run lead.
Ichiro made a highlight-reel catch in the bottom half of the frame. Encarnacion hit a ball to the right-field corner but the Japanese star tracked it down on the fly before crashing into the padding underneath the seats.
Lawrie hit his 11th homer of the season to deep left-centre field in Toronto's three-run fifth. Hughes gave up three straight two-out hits before being pulled, including Moises Sierra's RBI single that scored Escobar.
Hughes allowed five earned runs, eight hits, two walks and had four strikeouts.
Announced attendance was 31,418 on fan appreciation day.
Notes: Encarnacion left the game in the seventh. He was pulled as a precaution due to a tight muscle in the left shoulder area. ... The game took three hours 25 minutes to play. ...The Rogers Centre roof was closed. ... The Blue Jays have lost 10 of their last 14 games while the Yankees have won 11 of 15. ...The Blue Jays will close out the regular season with a three-game series against the visiting Minnesota Twins. Aaron Laffey (4-6) is the scheduled starter for Monday's opener. The Twins will counter with Esmerling Vasquez (0-2). The Yankees will finish off the season with a three-game home series against Boston.