The pair will miss the World Cup after being stretchered off against Italy.
Farrell, who worked with Gatland on the 2013 British & Irish Lions tour, says Wales should not be taken lightly.
"Warren will probably use a little bit of a backs-against-the-wall mentality which will strengthen them and galvanise them even more," he said.
"They are not down. They have a couple of guys who have come in who have got their opportunity and they are going to try and take that with both hands.
"Some people would say that it weakens them a little bit, but we don't see that. The strength of a team - the galvanisation of a team coming together - is more important than any individuals."
England and Wales meet at Twickenham on 26 September in what will be the second game of the tournament for both sides.
Webb is replaced in the Wales squad by Lions scrum-half Mike Phillips while Ospreys wing Eli Walker takes full-back Halfpenny's spot.
Farrell says Halfpenny, the player of the series for the Lions in 2013, is a sad loss for the tournament, after he suffered cruciate ligament damage on Saturday.
"He's an unbelievable professional," he added. "His attention to detail is absolutely second to none.
"He'll be a big loss to any side, he's a great player. And he will be sadly missed by the competition because we want to see the best out there."
However, Farrell feels fly-half Dan Biggar will be more than capable of kicking the goals in Halfpenny's absence.
He said: "Halfpenny's as good a kicker as there is in world rugby, there's no doubt about that. He's a phenomenal goal-kicker.
"But Dan Biggar is a very good goal-kicker. He's a long-range goal-kicker and he's very confident in taking the shots from anywhere. So they've got a pretty good replacement there."
And Farrell also believes Phillips will be a handful.
"He's not a bad replacement. An angry Mike Phillips - I suppose he would have been wanted to have been selected in the first place - he will probably have a point to prove.
"When he is in a determined mood he will probably be at his best."
England lock Geoff Parling described the news of Halfpenny and Webb's injuries as "horrendous".
He said: "You never want to see any rugby player get injured, but especially not in the last match before the World Cup."
Parling played with Halfpenny on the 2013 Lions tour and said he was "gutted" for the full-back.
"He's a really good bloke and I wish him a speedy recovery," he said. "He'll definitely be back, he's a quality guy."
Meanwhile, England fly-half George Ford has praised the impact of centre Sam Burgess, who came on as a replacement in Saturday's 21-13 win over Ireland, as "phenomenal".
"He's a winner," Ford said. "He's constantly talking. Breaks in play, he'll go up to the lads and energise them.
"His attributes in terms of carrying and tackling are there to see, but it's the things that people maybe don't see - his attitude and the drive that he gives to the team are pretty phenomenal."
Wales boss Warren Gatland will use the injuries to Rhys Webb and Leigh Halfpenny to galvanise his side, says England defence coach Andy Farrell.