Having to play catch-up against the nation's top team was the difference as the Wildcats came up short in Saturday's 45-31 loss.
The sophomore quarterback completed 24 of 43 passes for a career-best 390 yards and two touchdowns. Towles also rushed for 76 yards on 23 carries and two scores, including a 48-yard run to set up his own 10-yard touchdown in the third quarter.
''They're a really good team and they're No. 1 in the country for a reason. We made a lot of plays, we just didn't make enough. We fought like I knew we would. We just didn't make enough plays.''
Kentucky coach Mark Stoops agreed.
''We were inconsistent,'' Stoops said. ''He was inconsistent. We needed to play better all the way across the board. But I thought Patrick did some good things.''
Kentucky's last win over a top-ranked opponent was a 43-37, triple-overtime defeat of LSU in 2007. The Wildcats couldn't pull off the same feat against a Bulldogs team that got timely scores all four times Kentucky got within a touchdown.
Christian Holmes sealed the game for Mississippi State (7-0, 4-0) with a 61-yard kickoff return for a touchdown with 2:22 remaining. The Bulldogs earned their sixth straight win over the Wildcats and evened the series at 21 wins each.
Kentucky (5-3, 2-3) lost its second straight and fell to 3-12 all-time against the No. 1 team.
''We did not play well enough to win, to beat the No. 1 team in the country,'' Stoops said. ''I felt like our guys, they went about their business. Their minds were right. Their hearts were right. They tried the best they could. They (the Bulldogs) were a better football team.''
Prescott, the Heisman Trophy hopeful, and Robinson answered with TDs on three occasions. Prescott ran for TDs of 2 and 11 yards and hit Brandon Hill for an 8-yard TD.
Robinson's 73-yard touchdown run early in the fourth for a 38-24 lead proved critical after Towles' 4-yard TD dive with 2:31 remaining brought Kentucky within 38-31. He rushed for 198 yards on 23 carries and capped Mississippi State's opening drive with a 12-yard TD run.
Kentucky sacked Prescott three times and intercepted him once, but he completed 18 of 33 passes for 216 yards and rushed for 88 yards on 18 carries. Mississippi State outgained Kentucky 542-504 and needed every yard.
''They made more plays than us,'' defensive back Blake McClain said. ''That's all it was.''
But typical of a competitive series where four of the past six games have been decided by a touchdown or less, Mississippi State couldn't exhale until the final gun.
Fortunately for the Bulldogs, they showed no rust from a bye and put the Wildcats in comeback mode from the start. After forcing Kentucky to punt on its opening drive, Prescott completed his first five passes for 56 yards to quickly move Mississippi State into Kentucky territory.
But Prescott's biggest play was recovering his own fumble at the Wildcats 13 after a 3-yard gain, extending the drive and setting up Josh Robinson's walk-in touchdown on the next play.
Kentucky responded quickly with Towles' 67-yard TD pass to Demarco Robinson that got the homecoming crowd of 64,791 back in the game. If going up to snag the high pass wasn't impressive enough, Robinson managed to keep his feet inbounds as he came down while shaking off the defender.
Mississippi State scored 10 straight points, converting Braylon Heard's fumble into Evan Sobiesk's 26-yard field goal and capping a 68-yard drive with Prescott's 2-yard run. Austin MacGinnis' 34-yard field goal brought Kentucky within a touchdown and the Wildcats got another chance to narrow the lead before halftime.
Mississippi State opened the second half strongly behind leading rusher Robinson, who got the Bulldogs into Kentucky territory with three straight carries for 34 yards to the 28. Prescott finished things off five plays later with a bullish 11-yard TD run for a 24-10 lead that still wasn't safe.