Deeney, a 57th-minute substitute for Gabriele Angella, beat Andy Lonergan with a low shot from 16 yards to give the Hornets victory in a breathtaking encounter.
Zach Clough’s second equaliser with five minutes left brought the sides level at 3-3 after Joel Ekstrand’s first goal in nearly two years had threatened to give Watford all three points.
Watford had taken the lead through Odion Ighalo and although goals from Clough and Adam Le Fondre had turned the tide, the visitors went back in front thanks to strikes from Almen Abdi and Ekstrand before the late drama.
Bolton goalkeeper Lonergan, one of only three survivors from the Trotters starting line-up at Vicarage Road last August, blocked Ikechi Anya’s shot and Matej Vydra’s follow-up.
But Le Fondre spurned one great opportunity for Wanderers, skipper David Wheater narrowly headed wide during an entertaining start to the game, while on-loan Manchester United teenager Saidy Janko blasted another opening narrowly wide.
Wheater, however, was then too easily beaten by Ighalo’s turn inside the area after the Hornets ace ran on to Ben Watson’s through ball to net his 15th league goal of the campaign.
Bolton came from behind to beat Fulham 3-1 four days earlier and responded with purpose. Watson kicked Le Fondre’s 18-yard drive off the line with Heurelho Gomes beaten before the ex-Spurs custodian finger-tipped away Barry Bannan’s long-range effort.
But seven minutes from half-time came a contentious Clough equaliser. Le Fondre seemed to be stood in an off-side position as Janko played in Liam Feeney and assistant referee David Benton clearly raised his flag.
Watford’s defenders hesitated as Feeney crossed into the area for Clough to sweep home his fourth goal in six games. Despite visiting protests referee Geoff Eltringham overruled his colleague.
There was nothing contentious about Le Fondre’s second in as many games, with the on-loan Cardiff marksman superbly turning in Feeney’s cross from the opposite flank from 10 yards.
Watford were quickest to settle after the break and only Lonergan’s acrobatics kept out Anya.
Wanderers should have put the result beyond doubt as twice in quick succession Le Fondre failed to beat Gomes from close range.
Both keepers were in outstanding form with Lonergan – on his 50th league appearance for the club – foiling Abdi with a brace of excellent saves.
In-between, Watford replaced Watson and Vydra with Fernando Forestieri and Daniel Tozser as they pressed to get back in the game.
And the bold move paid off with two goals from Abdi and Ekstrand.
Ekstrand, 26, headed in Abdi’s cross 16 minutes from time to double his goal tally for the club after Swiss star Abdi had netted Watford’s equaliser five minutes earlier, finally getting the better of the outstanding Lonergan.
However, Bolton were not finished and from winger Feeney’s third assist of the game Clough, 19, moved to become the club’s joint top scorer.
The celebrations, however, were then cut short by Deeney’s calm finish into the corner.