Mandel evened his record at 2-2, allowing two runs on five hits over 6.1 innings of work, as the Huskers broke the shutout in the sixth on Brandon Buckman's two-run single.
Sunday's loss marked the first time NU had been swept since dropping a three-game series at Baylor in the 2004 campaign, and the first-time the Huskers' had been run-ruled since the 1998 season.
NU starter Johnny Dorn (9-3) was bidding to become only the second Husker to win 10 games in consecutive years, but could not get out of the third, as he allowed six runs on six hits to see his personal six-game win streak snapped.
The Bears wasted little time getting on the board, as Kevin Russo opened the game with infield single before coming home on Zach Dillon's two-run homer to right to spot BU a quick 2-0 lead.
Dillon paced a balanced Bear offense by going 2-for-2 and scoring four runs, as four Bears had two RBIs.
Baylor continued to hit in the second, as consecutive doubles by Ben Booker and Mike Pankratz made a 3-0 advantage. The Bears continued to threaten, as Beamer Weems sacrificed Pankratz to third, but Dorn retired the next two hitters to get out of the inning.
The Bears chased Dorn in the third, as his 2.1 inning stint was the shortest of his career. Dillon opened the inning with a double to left and scored two batters later as Opitz misplayed a hard-hit grounder to second. Tim Jackson made it a 5-0 game, as he plated Gerdes with a double in the gap to end Dorn's day after 14 batters. BU pushed across another run later in the inning on Pankratz' RBI double to center.
The Bears continued their offensive production in the fourth off of reliever Jon Klausing with three more runs, including an RBI bunt single by Seth Fortenberry and a two-run triple by Gerdes to make it 9-0.
The Huskers got on the board in the sixth, getting three consecutive hits, including a two-run single by Buckman to get on the board. A single by Nick Jaros and a double by Ryan Wehrle put runners on second and third before Buckman singled.
Wehrle led NU with a pair of hits and now has a team-high 25 multi-hit games this season.
The Bears added three more runs in the sixth on a Kevin Russo homer and TBI singles by Jackson and Booker.
The Huskers return to action on Tuesday night, as they travel to Omaha's Rosenblatt Stadium to take on the Creighton Bluejays. First pitch is set for 7p.m. and the game will be carried across the state on the Pinnacle Sports Network. The game will also be shown on the University of Nebraska's Educational Television state-wide network.