Paul had 16 points, 13 assists, six rebounds and an apparent swollen lip after Knicks center Robin Lopez hit him in the face in the third quarter.
Jordan responded by shoving Lopez from behind, they shoved again later, and Jordan was called for a technical foul.
"I was just upset," he said. "Chris is the smallest dude on the floor, you know what I'm saying? So we've got to protect him."
Doing so will cost Jordan $3,000, the penalty for his eighth technical of the season.
Jordan joked he would ask for his reimbursement on the flight to Toronto, then thought better of it when realizing Paul might then stop throwing him those perfect lob passes.
"If I've got to give up the lobs, then I'll just take the fine," Jordan said.
The duo hooked up on a few alley-oops during the game as Jordan didn't have to work hard to improve his NBA-leading field-goal percentage to 72.1 percent.
Paul was just 1 for 8 in the first half, then scored 14 points in the third quarter, perhaps fired up by the shot from Lopez.
"Chris is a competitor, so if I'm going to turn a guy on it would probably not be him," Clippers coach Doc Rivers said.
Paul Pierce finished with 13 points as the Clippers rebounded from Thursday's 115-102 loss in Cleveland to win for the 12th time in 14 games. Los Angeles shot 56.6 percent from the field.
"A team that has a roster constructed like theirs, the way that they lost last night, tonight was their opportunity to right what happened last night," Knicks coach Derek Fisher said.
Carmelo Anthony scored 16 points, but shot just 4 for 12 for the Knicks (22-23), who were trying for a third straight win that would have moved them over .500. Kristaps Porzingis shot even worse, going 4 for 17 while finishing with 13 points and eight rebounds.
The Knicks were within five points early in the second half before the Clippers blew it open during a third quarter that lasted more than a half hour, thanks to a lengthy video review preceding Lopez's ejection, and a few intentional fouls of Jordan, who went 6 for 12 from the line.
Los Angeles beat the Knicks for the seventh straight time, the longest active winning streak by any team against New York and the Clippers' longest in franchise history.
Jordan finished with eight rebounds, ending his career-best streak of double-doubles at 10.
Clippers: With a game at Toronto on Sunday, Rivers said the Clippers would fly out Friday night after the game rather than wait and risk the impending snowstorm forcing them to stay in New York — even though he joked that was probably what the players would want.
Knicks: Lance Thomas missed a second straight game with a sore left knee. Fisher said the reserve forward was getting better, but wasn't sure if he could play Saturday at Charlotte. ... The Knicks fell to 7-3 in the first game of back-to-back sets. The back end is in Charlotte — provided the Knicks were able to get there with the weather.
Lopez's take on the altercation: "Things were getting pretty chippy out there. It happened so fast. Kind of hard to recall, but maybe I overreacted a little bit. What happened, happened. I'm OK with it."
Pierce also was called for a technical foul.
The Clippers traded Josh Smith to Houston earlier Friday. Smith ended last season with the Rockets before signing with the Clippers. "Obviously, I wanted Josh out to work out," Rivers said. "It just didn't for us." Smith averaged 5.7 points and 3.7 rebounds, and Rivers said he didn't ask out after falling behind backup center Cole Aldrich in the rotation.
Clippers: Visit Toronto on Sunday.
Knicks: Visit Charlotte on Saturday.