Chelsea were 4-0 in front and cruising to victory when coach Guus Hiddink replaced Didier Drogba and Frank Lampard in the 65th minute.
Two goals from Drogba, a Lampard penalty and Michael Ballack's first league goal of the season had put Chelsea in total command.
But battling Bolton scored three times in 11 minutes through Andy O'Brien, Chris Basham and Matt Taylor to give the Blues an almighty scare.
The result leaves Chelsea just four points behind leaders Manchester United at the top of the Barclays Premier League.
United also have a match in hand but Chelsea are determined to keep the pressure on Sir Alex Ferguson's team.
Bolton had the better of the opening exchanges with Chelsea looking a pale shadow of the side that demolished Liverpool in the Champions League in midweek.
The home side were almost caught out in the second minute when a free-kick from Taylor was palmed away by goalkeeper Petr Cech as it arrowed towards the top corner.
Chelsea's best response was a 20-yard drive by Drogba that Bolton goalkeeper Jussi Jaaskelainen did well to keep out.
But Bolton continued to take the match to the home side and in the 15th minute Kevin Davies sent a 20-yard volley fizzing beyond Cech's right-hand upright.
Bolton went close again in the 21st minute when Ballack lost possession to Gardner.
The Bolton midfielder set off on a mazy run but was forced to lay the ball off to Davies on the left.
When his cross arrived Taylor headed inches over with Cech beaten.
But Lampard almost made Bolton pay when his 30-yard free-kick squirmed under Jaaskelainen's body and out for a corner.
Chelsea were not afraid to shoot from range and John Mikel Obi, back in the side in place of Essien, brought another fine save from Jaaskelainen.
But the goal Chelsea had threatened for some time finally arrived in the 40th minute.
Ballack began the move by setting Salomon Kalou free on the right and the Ivorian's low cross back into the penalty area was fired into the roof of the net by the German midfielder.
Kalou broke free again moments later but this time his low cross was just inches behind the lurking Drogba.
Gary Megson's side had struggled to cope once the home side had increased the tempo of the game but Davies almost equalised when he sent a right-foot drive inches wide of an upright in stoppage time.
Chelsea went two goals in front in the 48th minute when they punished Bolton for some poor defending.
Jlloyd Samuel brought down the marauding Kalou on the right-hand edge of the penalty area and when the free-kick was played into the box Drogba's left-foot sent the ball into the roof of the net.
In the 59th minute Chelsea were awarded a penalty when Gretar Steinsson handled Lampard's attempted pass and the England midfielder stepped up to send Jaaskelainen the wrong way from the spot.
Bolton's dismal afternoon got worse in the 63rd minute when a corner from Malouda was headed down by Ivanovic and Drogba reacted quickest to guide the ball into the net for Chelsea's fourth.
The goal was the signal for Hiddink to rest some of his players ahead of their Champions League quarter-final second leg on Tuesday.
Deco and Nicolas Anelka were introduced into the action in the 65th minute for Lampard and Drogba respectively and it almost cost Chelsea dearly.
The changes removed the thrust out of the Chelsea attack and Bolton began to enjoy more possession and belief.
Ballack had to clear a Davies header off the line before O'Brien took advantage of a fumble by Cech to score in the 69th minute.
Bolton added a second in the 74th minute when Basham got on the end of a Davies header to guide the ball home.
Incredibly, Bolton made it 4-3 four minutes later when Taylor headed home a flick-on by Davies.
Malouda missed an injury-time chance to finish Bolton off for the second time but Jaaskelainen saved superbly.
But more drama was to follow when Deco cleared off the line from Gary Cahill with virtually the last kick of the game to deny Bolton one of the most sensational comebacks of the season.
