Alonso then fell to the ground in pain.
"We're out there competing and that's a big point in the game and I made a big mistake," Upton said afterwards. "I was pretty upset about it.
"It's childish. I've got to do better than that and not make that mistake again."
Alonso was attended to by team trainers and was later looked at by the Rockies' medical staff which deemed him not to have concussion-like symptoms.
The Padres said they will re-evaluate Alonso Sunday morning.
"I was just watching the game and felt something just hit me right across the head," Alonso said. "But it's part of the game. Guys get upset. I'm fine. Luckily, everything checked out well. We're going to move on."
Alonso was asked if he spoke with Upton after the incident.
"We discussed that," he said. "I don't think you guys [need to] know what was said. We talked about it, and it's all good."
Alonso was replaced in the bottom of the inning on defense by Derek Norris, who moved from catcher to first base. Austin Hedges then entered the game to catch.
The incident didn't sit well with Padres interim manager Pat Murphy.
"It happens. I don't approve of it. I don't think it's great. I think we can see what can happen. It's really unacceptable to do it around other people," Murphy said.
"Most of the time, showing that type of anger and that type of stuff is not healthy in my mind at all. I don't think it's a sincere form of handling a result. I don't see any place for it."
Corey Brock is a reporter for MLB.com. Keep track of @FollowThePadres on Twitter and listen to his podcast. This story was not subject to the approval of Major League Baseball or its clubs.