Connor Martin (seventh, 16:43.96) Ethan Samels (eighth, 16:46.07), Brendan O'Brien (ninth, 16:46.97) were in the top five for the Lions, whose 30 points were ahead of second-place Towson (55).
Sam Merng (11th, 17:05.43) and Alex Ozbolt (12th, 17:16.97) also ran for the champion Lions.
Catonsville was third (125), followed by Franklin (140) and Hereford (144).
"Ellis ran a heck of a race. He is having a heck of a season so you take your hat off to a guy like that for being able to win the race and beat Matt," Dulaney coach Chad Boyle said. "As a team we did a really great job packing it in."
Boyle's goal was to have his fifth runner be within 30 seconds of the top Lion.
"That is pretty tough to do when you have a front runner like Matt," Boyle said.
Owens and Ellis were leading most of the race with Owens ahead slightly through the two-mile mark.
"I knew going in that it would just be me and Matt Owens and going through my head I wanted to try and pass him as soon as possible, but that didn't end up working out, especially in the middle of the race," Ellis said. "He just kept countering my moves and so I decided I had to outkick him at the end."
"Each one of those surges probably put a little bit into Matt that he was going to be able to use at the end of the race," said Towson coach Gil Stange, who saw his senior's potential when he won a regional title during the outdoor track season as a junior and ran 9:49 at the state meet. "That 9:49 at states was a springboard to serious work in the summer."
Ellis is the sixth Baltimore County champion from Towson High since 1948 and the first since Mason Campbell in 2006.
Other top 25 finishers for second-place Towson included: Sushant Dhaurali (10th, 16:58.34), Vincente Iglesias (13th, 17:24.40), Jack Morgan (14th, 17:26.34), Liam Jones (17th, 17:33.20), Cory Parts (21st, 17:47.51) and Tyler Paul (22nd, 17:48.97).
Catonsville's Drew Nicolaus (24th, 17:52.47) was the only other Comet to place in the top 25.
Hereford senior Kelly Wesolowski (18:06.14) won the girls race in convincing fashion.
"It's exciting," Wesolowski said. "Last weekend I ran a 17:41 and that really boosted my confidence for this race."
Hereford's Emily Konkus (19:12.77) and Dulaney's Jessica Meek (19:18.57), Dorrie Gaeng (19:35.61) and Brooke Ruffin (19:48.40) completed the top five.
Destiny Clinton (11th, 20:28.23) and Rachel Krug (12th, 20:29.98) also placed in top five for Dulaney, whose 35 points was one less than runner-up Hereford (36).
Meghan Robinson (16th, 20:50.20) and Charlotte Northey (21:46.18) completed the top seven for Dulaney.
"It was just a phenomenal team effort," Boyle said. "Destiny Clinton ran the race of her life and Rachel Krug ran the race of her life. That's what you need to upset Hereford because they are a phenomenal team. We knew all of us had a role and we had to run our best and they did."
The coach, in his 18th cross-country season at Dulaney, knew what they had to do to pull it out.
"They had to finish well and they finished that last mile very well," Boyle said.
They also got off to a good start with a pep talk from former Dulaney High two-time Maryland state cross-country champion Amanda Pagon.
Pagon, known as Amanda White before she married, was the best cross country runner in the nation when she won the Kinney national championship meet in 1992.
The Virginia resident was in town for a Hall of Fame dinner at Dulaney High on Friday night and had some advice for the lady Lions on race day.
"I was yelling at those girls and I talked to them before the race and I said, 'This is your course.'" Pagon said.
Like Amanda White was back in the early 1990's, Wesolowski was in control of her race from start to finish, but Hereford coach Adam Hittner didn't plan on having Wesolowski win the girls' individual race by over a minute.
"We were trying to get her to go a little slower," said Hittner, noting she ran the first mile in 5.40. "We wanted her to take it easy and get the win and save something because she wants to run Nike regionals and nationals. She has a lot of good races left in front of her."
Despite not winning its second straight Baltimore County crown, Hittner and coach John Roemer will have the Hereford girls ready for the rest of the postseason.
"We will go to the state meet and run our best seven and hopefully come away with the trophy there," Hittner said.
The four runners for second-place Hereford behind Wesolowski were Emily Konkus (second, 19:12.77) Kelly Shearer (eighth, 19:59.90), Nicole Burkoski (10th, 20:15.38) and Hannah Ace (15th, 20:46.93).
Lillian Behan (19th, 21:04.11) and Hannah Weeren (30th, 22:08.22) also ran for the Bulls.
Towson (67), Catonsville (134) and Franklin (134) completed the top five in the girls' team standings.
Towson was paced by top 25 finishes from Karen Prem (sixth, 19:52.86), Jaqui Sheedy (seventh, 19:54.99), Lauren Miller (14th, 20:40.70), Sydney Conboy (18th, 21:03.36), Emily Stange (22nd, 21:32.32) and Amelia Kline (23rd, 21:35.95).
"The roles this season have been sorting out and now, here we are in the championships, and it clicked," said Stange, whose Generals will host the regional meet on Nov. 3.
Catonsville's top 25 finishers were sophomore Eva White (17th, 20:57.15) and senior Anna Piermattei (21st, 21:26.94).