Maguire rides for northern trainer Ferdy Murphy
The Irish jockey reached the milestone with victory on Fiori at Carlisle on Thursday, yet still ended up in trouble with the stewards.
He was given a rousing reception by racegoers as he returned to the winner's enclosure, and threw his whip into the crowd.
But the stewards suspended him for one day (December 13) for using his whip with excessive frequency in the race.
Just 24 hours earlier, he was in trouble with the whip after lashing out at fellow rider JP McNamara, a close colleague.
He hit him on the back with his whip after the John Wade Haulage Ltd Novices' Hurdle at Wetherby.
Maguire reached the 1,000 mark on the 9-4 joint-favourite Fiori, who made virtually all the running to win the Viacom Outdoor Handicap Hurdle.
The jockey joins Richard Dunwoody, Peter Scudamore, Tony McCoy, John Francome, Stan Mellor and Peter Niven as the only National Hunt riders to make it to four figures.
Maguire paid tribute to the North Yorkshire-based trainer Ferdy Murphy, who snapped him up on a three-year contract in 2000.
"Since I started riding for Ferdy in the north I can honestly say that I have never enjoying my racing more," he said.
"I have a great team behind me and there are no thoughts of retiring."
The 1,000th win marks a high point in a rollercoaster decade for Maguire since he burst onto the scene by winning the National Hunt Chase at Cheltenham on Omerta for Martin Pipe in 1991.
His numerous big-race winners have included Cool Ground, who sprang a 25-1 surprise in the 1992 Cheltenham Gold Cup.
But the full jockeys' title has eluded him, most famously in 1993-4 when he lost out by just three winners - 197 to 194 - to Richard Dunwoody.
Maguire was also dogged by injuries in the mid-1990s.
He split from trainer David Nicholson in 1998, but then teamed up with Murphy .
Maguire landed in trouble on Wednesday when he lashed out after finishing fourth on Inching Closer.
He appeared to be angry that McNamara, who rides regularly for Murphy, had hung right on the winner Benbyas and into his mount in the finishing straight.
The stewards inquired into the incident and banned Maguire for six days - December 7-8 and 10-13.
As a result, he will miss the big Tingle Creek meeting at Sandown.
Murphy insisted all was well between the pair on Thursday.
"They went out and had a cup of coffee last night so they are perfectly all right - not a bother on either of them," he said.
And the trainer saluted his stable jockey, calling him "a great grafter".
"I don't know how many winners he has ridden for me but there have been quite a few I can tell you - he is the perfect stable jockey," said Murphy.
Maguire's colleague Tony Dobbin added his own tribute.
"For someone like him to have ridden 194 winners in a season and still not been champion is a travesty, he deserves to be a champion jockey," said Dobbin. said. "He is a fantastic rider, his record shows that and he is and always has been a very hard man to beat ."