Wood hit his homer of the season and fourth of his career, managing to clear the left-field bleachers with a drive that actually ended up landing on Waveland Avenue.
After the game, Wood said he was thinking about a home run, but it wasn't the one he himself hit.
With two outs in the seventh inning, rookie Juan Lagares connected off Wood's pitch for his first big league homer. The two-run shot tied the game, and Daniel Murphy hit a leadoff home run in the eighth that sent the New York Mets over Chicago 4-3 Sunday.
"As soon as it left the hand, I didn't like it," Wood said. "I was hoping he would pop it up or something. But he didn't. He put a good swing on it. Hit it out of the park to tie the ballgame."
Wood said the 2-2 pitch was a changeup that he tried to get down, but instead left up over the plate.
Overall, Wood did well on the mound, giving up three runs and five hits in seven innings, while striking out three and walking two.
It was Wood's ninth consecutive quality start to open the season. The last Cubs starter to begin a season with at least nine straight quality starts was Mordecai "Three Finger" Brown in 1908.
"Woody pitched another great game," Cubs manager Dale Sveum said. "Obviously we'd like to have that one pitch back. It was the last batter he was going to face and he threw his worst pitch of the game in that situation. That was unfortunate, obviously. We pitched great, we just couldn't keep the ball in the ballpark the times we needed to."
Murphy homered off Kyuji Fujikawa (1-1) as the Mets got their first series win at Wrigley Field since 2007. Murphy has homered twice in three games and has an eight-game hitting streak.
Scott Rice (2-3), who leads the majors with 25 relief appearances, pitched two scoreless innings for the victory. Bobby Parnell tossed a perfect ninth to earn his sixth save in eight opportunities.
The Cubs extended their lead to 3-1 in the sixth on Ryan Sweeney's leadoff homer. It was his first home run since July 27, 2011, when he played for Oakland.
Mets starter Dillon Gee allowed three runs and eight hits in five innings. He has allowed nine runs in his last nine innings and hasn't won since May 1.
The Cubs missed out on several other scoring opportunities against Gee. Sweeney tried to stretch a leadoff double into a triple in the fourth but was thrown out at third. The Cubs failed to drive in runners from third in the first, fifth and sixth.
"It's too bad we didn't win that game today because of Woody's home run," Sveum said.
NOTES: The Cubs announced after the game that reliever Michael Bowden will be designated for assignment to make room for Matt Garza, who is coming off the disabled list on Tuesday to face Pittsburgh in his season debut. ... Cubs 1B Anthony Rizzo struck out in the first inning, ending 39 straight plate appearances without a strikeout. ... Cubs RHP Carlos Villanueva was available. He moved to the bullpen to make room for Garza, who strained a back muscle in spring training. Villanueva (1-3) hasn't won since April 18. He has made 245 of his 309 career appearances as a reliever.
The Associated Press contributed to this report.