Shishkin had to work hard before getting his first win of the season and put himself well in contention for next month's Cheltenham Gold Cup.
The Nicky Henderson-trained horse had unseated jockey Nico de Boinville at Kempton last time out after refusing to race in his season-opener at Ascot.
But the 8-11 favourite outstayed both Hitman and Protektorat to land the Denman Chase at Newbury.
"What we saw today was a stepping stone to the Gold Cup," said De Boinville.
"There is definitely more to come."
There had been questions of the 10-year-old after the King George VI Chase on Boxing Day, where he stumbled after the second-last when looking a likely winner.
But this time he started smoothly and apart from a minor error early on, he tracked leader Protektorat for a long time, then took the lead at the second-last and went on to win by four-and-a-quarter lengths.
"He is a fantastic horse but he just takes a bit of knowing," the winning jockey told ITV Racing. "It was nice to atone for Boxing Day.
"He galloped to the line and it was a case of keeping him interested and happy."
Henderson, who won the race for the third time, admitted he was relieved.
"I think this race will do him a lot of good. He needed the run," he said
"Apart from one fence he jumped great. We are in control of him now and he is behaving our way."
De Boinville and Henderson made it a double with victory for 11-2 shot Iberico Lord in the Betfair Hurdle ahead of L'eau Du Sud, Go Dante and Doddiethegreat.
Edwardstone cruised to victory in the Game Spirit Chase for jockey Tom Cannon and trainer Alan King.
The 11-10 favourite won by 40 lengths from the only other finisher Funambule Sivola, with Boothill falling two from home and Amarillo Sky pulled up by jockey Joe Tizzard.