Wells hit a three-run homer off Bruce Chen (6-5) in his first at-bat since returning to the team after missing three games to be with his wife, who gave birth to a boy this past Friday.
Wells entered the game hitting just .220 with runners in scoring position.
"Vernon's a pretty easy-going guy. Of course, he gets in there for his first at-bat and jumps on the first pitch he sees and hits it out of the park," Lilly said. "That's the Vernon I know, right there."
One batter later, Hill hit his first major-league home run. Hill, a rookie, went 4-for-4 to establish a career high for hits and raise his average to .382. He also walked.
Lilly (5-7) allowed two runs on three hits in seven innings, lowering his ERA 6.08.
"He was outstanding. He came out and threw his fastball, he's got a great one and he's starting to believe in it again," Wells said. "If we can get him going it will be a key for us."
The 28-year-old left-hander struck out a season-high 10 and walked two, the sixth time in his career he's struck out 10 or more and the first since Aug. 20 when he fanned a career-high 13 against Boston.
Marrero hit a two-run homer for Baltimore, which had won five of six. The three hits tied the Orioles' season low, done three times previously.
Chen allowed a season-high six runs on nine hits in five innings.
"Sometimes I have a tendency to be lazy and not finish my pitches," Chen said. "Obviously, I didn't have my A game. They hit me and they hit me good."
Wells said he felt relaxed after a long weekend of little sleep. His wife, Charlene, had an emergency C-section.
"That's a major surgery, but everything went well," Wells said. "You can relax knowing your baby is healthy. You can just come out here and have a good time, but at the same time you miss being with them."
Marrero homered off Lilly in the second, but Toronto took a 6-2 lead in the fifth on Shea Hillenbrand's RBI double and Hill's run-scoring single.
Hillenbrand added a solo homer off James Baldwin in the eighth.
Manager John Gibbons said shortstop Adams is going to start seeing a lot more action against left-handers. Gibbons has decided that Adams is ready for full-time duty. The left-handed hitting rookie had been splitting time with the right-handed John McDonald
... Orioles second baseman Brian Roberts returned to the starting lineup after not starting Sunday because of a sore back that's been bothering him for more than a week.