Yordan Minev fired in the only goal in the final moments after the Bulgarian champions had dominated the second half, moving the team up to second in Group B, behind defending European champions Real Madrid.
Here, Sports Mole takes a closer look at the outcome in Sofia.
On target: 7
On target: 3
Was the result fair?
It is a difficult one to call as Ludogorets were by far the better side as a result of the early red card, but Basel should never have been reduced to 10 men. Serey Die barely made contact with Cosmin Moti, but his dismissal left the visitors having to defend for the majority of the match, and ultimately left them with too much to do. Had the Swiss side continued with 11 players, they would probably feel hard done by, but given Ludogorets's performance, the victory was fair.
The home side had made a bright start and created a couple of chances prior to the red card incident, but struggled to adapt to playing against 10 men in the first half. However, they rallied superbly after the break to really stretch their more-decorated opponents, and ultimately wore them down. They could, and probably should, have won by a greater margin given the number of chances that they created, but they looked delighted with their first Champions League win when the full-time whistle went.
Basel had looked rather scrappy and unsettled prior to Die's dismissal, but they responded well, defending superbly for much of the match. The Swiss champions tried to attack even after being reduced to 10 men, but struggled to maintain their effort after the break, and some weary defending ultimately allowed their opponents in for the winner late on.
Sports Mole's man of the match
Fabio Espinho: The midfielder looked sharp in the first half for the home side, creating a series of chances for Marcelinho, before taking a more central role after the break. He forced a couple of saves from Tomas Vaclik, while seeing another few shots fly wide, and worked well with Roman Bezjak and Dani Abalo. Espinho may not have scored the winner, but he played a huge role in breaking down the Basel defence.
It may be a little harsh to lay the blame at Serey Die's door, as he really should not have been shown a straight red for the challenge that got him sent off. However, the referee had warned Basel that their challenges were getting a little dangerous, while Die had been lucky to escape a yellow a few minutes earlier. Regardless of the accuracy of the officiating, it was a needless risk so early in the game that left his teammates with a mountain to climb.
German referee Deniz Aytekin will cringe when he sees some of the mistakes he made this evening. He was too lenient with some of Basel's early tackles, made a mistake in sending Serey Die off, and then missed a blatant penalty a few minutes later when Derlis Gonzalez was pushed in the Ludogorets box. It would be no exaggeration to say that the official made a mistake with every major decision that he had to take this evening.
Ludogorets: The Bulgarian champions host Cherno More in the league this weekend, and travel to Marek next Friday ahead of a rematch with Basel next month.
Basel: Basel are at home to Sion in the league this weekend, and have another league match and a domestic cup match before hosting Ludogorets on November 4.