Rodriguez hit an RBI single with two outs in the ninth that made it 7-5. Jorge Posada followed with a high infield pop and Rodriguez ran hard, cutting between Clark and shortstop John McDonald.
Replays showed Rodriguez shouting something, and Clark backed off at the last second. McDonald was only a few steps behind Clark, but couldn't make the catch and ball dropped for an RBI single.
"I just said, 'Hah!' That's it," Rodriguez said. "Sometimes it works, sometimes it doesn't."
McDonald started jawing with Rodriguez, and third base umpire Chad Fairchild got between them. Toronto manager John Gibbons came out to argue, and exchanged words with Rodriguez and third base coach Larry Bowa before leaving the field as plate umpire Eric Cooper intervened. Rodriguez stayed on the bag with a smirk.
When Jason Giambi stepped up to hit, he seemed to get into it with catcher Jason Phillips and Cooper settled them down.
Giambi followed with a two-run single. When the game ended, many of the Blue Jays stayed on the bench, staring at Rodriguez and the Yankees.
"They have their opinions," he said, adding he pulled the trick to help the Yankees "win a game. We're desperate."
Rodriguez said three or four times each week, opponents shout at him while he pursues foul pops near their dugout.
"It's not like he said, 'I got it,"' Yankees manager Joe Torre said.
It certainly was an adventuresome day for Rodriguez. He made the cover of the New York Post on Wednesday -- and not because of the Yankees' latest slump.
"STRAY-ROD" blared the Page 1 headline across a picture of A-Rod and an unidentified woman in Toronto earlier this week. "Alex hits strip club with mystery blonde," it continued.
"Absolutely no comment about anything personal and I certainly don't think this will be a distraction to our team," he said before Wednesday's win.
Rodriguez has been in the middle of an unusual, on-field dispute before. In Game 6 of the 2004 AL championship series, he slapped the ball from Boston pitcher Bronson Arroyo's glove, and was called out for interference.
Johnny Damon led off this game with a home run for the Yankees, who avoided falling nine games under .500 for the first time since they were 20-29 after play on June 20, 1995, according to the Elias Sports Bureau.
Robinson Cano hit three doubles and went 4-for-4 for the Yankees. Down 13½ games to Boston in the AL East, New York starts a three-game series Friday night at Fenway Park.
Pitching for the first time since May 26, Mariano Rivera recorded the final four outs for his fourth save in six chances.
New York took a quick lead against rookie Jesse Litsch (1-2), scoring five times in the first inning. Damon opened the game with his 22nd career leadoff homer.
Josh Phelps followed with a two-run single and Cano hit an RBI double, bringing Brian Tallet from the bullpen.
Making just his fourth major league start, Litsch allowed a season-high five runs on four hits.
Damon singled in the second for his 2,000th career hit.
Melky Cabrera singled home Cano in the sixth off reliever Josh Towers.
Yankees rookie Tyler Clippard (2-1) gave up three runs and four hits over five innings. He struck out three and walked five, but none of the walks came around to score.
Rios homered in the third. Toronto then loaded the bases with two outs but Clark flied out.
McDonald homered in the fourth and Stairs hit a two-run shot off reliever Brian Bruney in the seventh.
It was the first time Bruney had given up a run since April 23 at Tampa Bay. He had pitched 13 2/3 scoreless innings since.
- The Yankees and Toronto next play in mid-July.
- Jeter finished 0-4 with three strikeouts.
- Yankees OF Bobby Abreu got the night off.
- Reliever Brian Wolfe made his major league debut in the ninth, making him the 500th player in Blue Jays history.