The Orioles took advantage of a two-out throwing error by Jeter in the first to build a big cushion for Daniel Cabrera (5-1), who handed the Yankees (20-25) their fourth straight loss and sixth in seven games.
Kevin Millar and Luke Scott added tack-on homers for the surprising Orioles, who have won eight of 10. Jones finished with a career-high four hits and four RBIs.
With Baltimore up 9-0 in the third, Cabrera hit Jeter on the left hand with a 2-1 pitch and the star shortstop spun away in pain. New York manager Joe Girardi and a trainer came out to check on Jeter, who was quickly removed from the game.
X-rays were negative, and Jeter is day-to-day with a bruised hand.
In the sixth, New York reliever LaTroy Hawkins threw one pitch inside to Scott and then the next one over his head. Hawkins was immediately ejected by plate umpire Chuck Meriwether without a warning, while Scott and Hawkins began gesturing at each other.
Both benches and bullpens emptied as players spilled onto the field, but no punches were thrown. Hawkins was replaced by Edwar Ramirez.
The Yankees trailed 9-0 before Rodriguez even came to bat. Unable to overcome Jeter's miscue, Mussina (6-4) got only two outs against his former team - matching the shortest start of his 18-year career. The right-hander had won five starts in a row.
Aubrey Huff and Freddie Bynum had RBI singles in the first inning for Baltimore. After scoring the first run of the game, Brian Roberts added an RBI triple to cap the outburst.
After missing three weeks with a strained right quadriceps, Rodriguez returned to the cleanup spot and started at third base. He reached on an error in the second inning, grounded out in the fourth and hit a two-run homer in the sixth off Cabrera to make it 10-2.
Cabrera gave up five hits in seven innings, winning his third consecutive start.
Yankees left fielder Johnny Damon dropped a fly ball for an error with two outs in the second, leading to two unearned runs off Ross Ohlendorf.
New York had allowed five unearned runs all season before giving up eight Tuesday night.
