Stottlemyre was waiting for Wendelstedt to come to the mound before starting in on him. The pair walked toward home plate before Stottlemyre was given the heave-ho.
"I pride myself in throwing strikes," Haren said. "I don't walk people. That was only my 36th. The coaches came out and told them how they felt."
Hinch came out of the dugout to get between Stottlemyre and Wendelstedt and then asked for an explanation.
Wendelstedt held up four fingers as if to indicate he gave Stottlemyre four chances. Hinch then appeared to get irate, and it wasn't long before he joined Stottlemyre.
"My main problem was when you're supposed to defuse a situation, it wasn't defused," Hinch said. "I felt the two ejections didn't need to happen. I don't care how many games are left; I still have the same intensity and desire. ... I want the players to know we're going to fight to the very end. We ended up getting tossed."
Crew chief Dana DeMuth said Wendelstedt warned Stottlemyre four times and warned Hinch three times. The manager and pitching coach were the fourth and fifth ejections of the season for Wendelstedt.
Haren (14-10) gave up five runs on eight hits in his six innings. He walked one and struck out five as he dropped to 0-2 in his last three starts.
"It was just the one inning," Haren said. "I've been struggling the last few times out. I get into a jam and I can't get out. There was no doubt I was frustrated but I gathered myself and got the next two outs. It didn't linger. I still feel good. I'm just disappointed with the way I finished my season."
Justin Upton singled home two runs and Stephen Drew added an RBI single but it was a case of too little, too late. All the runs came in the eighth inning.
"Lincecum pitched well," Hinch said. "I didn't feel like he had his most dominant stuff but he's pretty effective even without his A-1 stuff. Premier pitchers around the league find ways to get outs."
The D-backs, who won their last two home games of the year, were swept for the eighth time.
"It's a big series in Chicago," Hinch said. "Right now we're going, or at least I am, into the offseason with a pretty sour taste in my mouth. Ending the season on a positive note is the goal and we have three games to prove it to ourselves."