Di Matteo's men could have gone above fourth-placed Tottenham, who lost to Norwich earlier on Monday, had they beaten their west London rivals.
But Frank Lampard's penalty -- his 150th Premier League goal -- on the stroke of half-time was cancelled out by Clint Dempsey's late header for Fulham.
The top three teams in the Premier League at the end of the season gain direct entry into the Champions League group stages, with the fourth-placed side set for the qualifying round.
This draw left Chelsea two points behind Tottenham, their opponents in an all-London FA Cup semi-final at Wembley on Sunday.
Di Matteo, interim manager following the sacking of Andre Villas-Boas, said Chelsea's habit of conceding late goals -- they've let in 20 in the final 10 minutes of games this season -- was frustrating.
"You look at it and we're closer to that fourth spot that we were," Di Matteo said as he tried to put Monday's result in the best possible light.
"We have to look at it positively," the Italian added. "We are closer now than we were a month ago.
"The biggest disappointment is that we conceded an equaliser late on. It's been a pattern this season, conceding late goals."
After the FA Cup semi-final, Chelsea face holders Barcelona in a Champions League semi-final first leg tie at Stamford Bridge on Wednesday, April 18.
Di Matteo is likely to be without Branislav Ivanovic for the Spurs game at Wembley, as he faces a misconduct charge over an off-the-ball clash with Wigan's Shaun Maloney on Saturday.
Full-back Ashley Cole could miss both matches with an ankle injury while fellow England defender John Terry is not at full fitness after suffering cracked ribs in Chelsea's Champions League quarter-final win over Benfica.
But Di Matteo added his side could cope with the strain, saying: "We've got a good squad, a squad full of good players. We will utilise them."
Fulham caused Chelsea problems throughout the first half and would have considered themselves unlucky to go in at half time a goal down.
The penalty appeared to have been given for Danny Murphy's tackle on Salomon Kalou, but replays suggested it was Stephen Kelly's challenge on the same player that saw referee Mark Clattenburg point to the spot.
Fulham had chances to equalise before United States international Dempsey's 16th goal of the season gained a point for the Cottagers.
"I'm just happy to create chances and if you do that you get a goal sometimes," said Dempsey.
Meanwhile, with his side mow in the top half of the table, Fulham manager Martin Jol backed former club Tottenham to finish fourth in the table despite their 2-1 defeat by Norwich earlier on Monday.
"I think Spurs will finish in the top four," said the Dutchman, in charge at White Hart Lane from 2004-07.
"They've got all the quality, which they have shown all season, except today (Monday) when they lost to Norwich."
Source: AFP
Source: AFP